HEADER VIRAL PROTEIN 18-FEB-21 7NKT TITLE RBD DOMAIN OF SARS-COV2 IN COMPLEX WITH NEUTRALIZING NANOBODY NM1226 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SPIKE PROTEIN S1; COMPND 3 CHAIN: AAA; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NEUTRALIZING NANOBODY NM1226; COMPND 7 CHAIN: BBB; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS SOURCE 3 2; SOURCE 4 ORGANISM_COMMON: 2019-NCOV, SARS-COV-2; SOURCE 5 ORGANISM_TAXID: 2697049; SOURCE 6 GENE: S, 2; SOURCE 7 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: EXPI293F GNTI-; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 12 ORGANISM_TAXID: 30538; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RBD, SARS-COV2, NEUTRALIZING NANOBODY, COMPLEX, NM1226, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.OSTERTAG,G.ZOCHER,T.STEHLE JRNL AUTH T.R.WAGNER,E.OSTERTAG,P.D.KAISER,M.GRAMLICH,N.RUETALO, JRNL AUTH 2 D.JUNKER,J.HAERING,B.TRAENKLE,M.BECKER,A.DULOVIC, JRNL AUTH 3 H.SCHWEIZER,S.NUESKE,A.SCHOLZ,A.ZECK,K.SCHENKE-LAYLAND, JRNL AUTH 4 A.NELDE,M.STRENGERT,J.S.WALZ,G.ZOCHER,T.STEHLE,M.SCHINDLER, JRNL AUTH 5 N.SCHNEIDERHAN-MARRA,U.ROTHBAUER JRNL TITL NEUTROBODYPLEX-MONITORING SARS-COV-2 NEUTRALIZING IMMUNE JRNL TITL 2 RESPONSES USING NANOBODIES. JRNL REF EMBO REP. V. 22 52325 2021 JRNL REFN ESSN 1469-3178 JRNL PMID 33904225 JRNL DOI 10.15252/EMBR.202052325 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28115 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1687 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1922 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.4150 REMARK 3 BIN FREE R VALUE SET COUNT : 122 REMARK 3 BIN FREE R VALUE : 0.4150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2503 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.68200 REMARK 3 B22 (A**2) : 0.68200 REMARK 3 B33 (A**2) : -1.36400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.179 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.145 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.113 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2629 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2286 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3570 ; 1.463 ; 1.656 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5306 ; 1.262 ; 1.578 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 323 ; 7.715 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;33.612 ;21.986 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 384 ;15.138 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;19.526 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 324 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2994 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 608 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 411 ; 0.190 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 21 ; 0.207 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1232 ; 0.176 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 136 ; 0.142 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1288 ; 3.653 ; 7.343 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1287 ; 3.640 ; 7.342 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1608 ; 5.262 ; 9.601 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1609 ; 5.264 ; 9.603 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1341 ; 3.990 ; 8.056 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1338 ; 3.870 ; 8.038 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1961 ; 5.482 ;10.305 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1956 ; 5.426 ;10.281 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 11 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : AA 332 AA 335 REMARK 3 ORIGIN FOR THE GROUP (A): 24.7403 -8.0440 40.7998 REMARK 3 T TENSOR REMARK 3 T11: 0.4335 T22: 0.4185 REMARK 3 T33: 0.4610 T12: 0.0430 REMARK 3 T13: -0.0576 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 1.5262 L22: 16.6277 REMARK 3 L33: 18.2101 L12: 2.9238 REMARK 3 L13: -4.7456 L23: -11.5694 REMARK 3 S TENSOR REMARK 3 S11: 0.1191 S12: 0.0135 S13: -0.2780 REMARK 3 S21: 0.3179 S22: 0.0662 S23: -0.3730 REMARK 3 S31: -0.1528 S32: -0.2562 S33: -0.1854 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : AA 336 AA 356 REMARK 3 ORIGIN FOR THE GROUP (A): 23.9572 -14.8402 21.3555 REMARK 3 T TENSOR REMARK 3 T11: 0.1393 T22: 0.4361 REMARK 3 T33: 0.1008 T12: -0.0965 REMARK 3 T13: -0.0064 T23: -0.0514 REMARK 3 L TENSOR REMARK 3 L11: 4.2219 L22: 10.6080 REMARK 3 L33: 4.5501 L12: -3.7277 REMARK 3 L13: -0.8394 L23: 1.2311 REMARK 3 S TENSOR REMARK 3 S11: -0.0464 S12: -0.6413 S13: 0.6095 REMARK 3 S21: 0.5957 S22: 0.0648 S23: -0.3732 REMARK 3 S31: -0.6014 S32: 0.5923 S33: -0.0184 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : AA 357 AA 396 REMARK 3 ORIGIN FOR THE GROUP (A): 13.7579 -15.4150 32.6247 REMARK 3 T TENSOR REMARK 3 T11: 0.3633 T22: 0.7664 REMARK 3 T33: 0.1247 T12: 0.1163 REMARK 3 T13: 0.0487 T23: 0.0231 REMARK 3 L TENSOR REMARK 3 L11: 6.9856 L22: 2.4046 REMARK 3 L33: 0.9887 L12: -1.0741 REMARK 3 L13: -0.4644 L23: -1.1267 REMARK 3 S TENSOR REMARK 3 S11: -0.2849 S12: -1.4964 S13: -0.1441 REMARK 3 S21: 0.7676 S22: 0.2626 S23: -0.0037 REMARK 3 S31: -0.2944 S32: 0.4509 S33: 0.0223 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : AA 397 AA 415 REMARK 3 ORIGIN FOR THE GROUP (A): 12.8601 -22.6064 16.0379 REMARK 3 T TENSOR REMARK 3 T11: 0.0322 T22: 0.2111 REMARK 3 T33: 0.1565 T12: -0.0044 REMARK 3 T13: -0.0290 T23: 0.0777 REMARK 3 L TENSOR REMARK 3 L11: 1.9108 L22: 6.6770 REMARK 3 L33: 5.9312 L12: -1.8625 REMARK 3 L13: -2.2153 L23: -1.8632 REMARK 3 S TENSOR REMARK 3 S11: 0.0973 S12: 0.0693 S13: -0.2840 REMARK 3 S21: -0.2742 S22: 0.1147 S23: 0.9369 REMARK 3 S31: 0.0086 S32: -0.1752 S33: -0.2120 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : AA 416 AA 518 REMARK 3 ORIGIN FOR THE GROUP (A): 20.0492 -24.4321 11.5165 REMARK 3 T TENSOR REMARK 3 T11: 0.0345 T22: 0.1668 REMARK 3 T33: 0.0612 T12: -0.0323 REMARK 3 T13: -0.0232 T23: 0.0517 REMARK 3 L TENSOR REMARK 3 L11: 3.6899 L22: 3.9860 REMARK 3 L33: 3.1607 L12: -1.2248 REMARK 3 L13: -2.4261 L23: 0.5622 REMARK 3 S TENSOR REMARK 3 S11: -0.0179 S12: -0.1810 S13: -0.2505 REMARK 3 S21: -0.2997 S22: 0.0782 S23: 0.1789 REMARK 3 S31: 0.0846 S32: 0.1419 S33: -0.0603 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : BB 1 BB 6 REMARK 3 ORIGIN FOR THE GROUP (A): -8.7025 -23.0787 21.3860 REMARK 3 T TENSOR REMARK 3 T11: 0.3330 T22: 0.3606 REMARK 3 T33: 0.3568 T12: -0.0388 REMARK 3 T13: 0.0094 T23: 0.0246 REMARK 3 L TENSOR REMARK 3 L11: 12.0814 L22: 10.3439 REMARK 3 L33: 7.5142 L12: -9.9780 REMARK 3 L13: 7.4581 L23: -8.1377 REMARK 3 S TENSOR REMARK 3 S11: 0.4075 S12: 0.2237 S13: -0.4344 REMARK 3 S21: -0.0487 S22: -0.3395 S23: 0.3838 REMARK 3 S31: 0.1348 S32: 0.5722 S33: -0.0680 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : BB 7 BB 17 REMARK 3 ORIGIN FOR THE GROUP (A): -25.3223 -8.7817 11.4117 REMARK 3 T TENSOR REMARK 3 T11: 0.2189 T22: 0.4439 REMARK 3 T33: 0.5037 T12: -0.0498 REMARK 3 T13: -0.0145 T23: 0.0738 REMARK 3 L TENSOR REMARK 3 L11: 0.0357 L22: 10.6456 REMARK 3 L33: 3.9138 L12: 0.1838 REMARK 3 L13: 0.3533 L23: 0.2039 REMARK 3 S TENSOR REMARK 3 S11: 0.0158 S12: -0.0421 S13: -0.0052 REMARK 3 S21: -0.8020 S22: -0.2325 S23: -0.3640 REMARK 3 S31: 0.1613 S32: -0.3335 S33: 0.2167 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : BB 18 BB 40 REMARK 3 ORIGIN FOR THE GROUP (A): -10.6009 -14.8753 19.0229 REMARK 3 T TENSOR REMARK 3 T11: 0.2498 T22: 0.1856 REMARK 3 T33: 0.4722 T12: -0.0648 REMARK 3 T13: -0.0174 T23: 0.0451 REMARK 3 L TENSOR REMARK 3 L11: 6.8955 L22: 3.0393 REMARK 3 L33: 7.3259 L12: -1.6268 REMARK 3 L13: 2.5108 L23: -1.9169 REMARK 3 S TENSOR REMARK 3 S11: -0.0162 S12: -0.3073 S13: -0.6898 REMARK 3 S21: -0.2387 S22: 0.1384 S23: 0.8280 REMARK 3 S31: 0.6238 S32: -0.4557 S33: -0.1222 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : BB 41 BB 45 REMARK 3 ORIGIN FOR THE GROUP (A): -7.7277 -11.7587 2.9823 REMARK 3 T TENSOR REMARK 3 T11: 0.3655 T22: 0.4057 REMARK 3 T33: 0.4025 T12: 0.0213 REMARK 3 T13: 0.0191 T23: -0.0460 REMARK 3 L TENSOR REMARK 3 L11: 4.3288 L22: 2.4838 REMARK 3 L33: 9.4146 L12: 2.5009 REMARK 3 L13: 0.6741 L23: 3.4791 REMARK 3 S TENSOR REMARK 3 S11: -0.3539 S12: 0.5706 S13: -0.1705 REMARK 3 S21: -0.2859 S22: 0.1752 S23: -0.0233 REMARK 3 S31: -0.2466 S32: -0.1779 S33: 0.1787 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : BB 46 BB 109 REMARK 3 ORIGIN FOR THE GROUP (A): -9.3360 -7.9494 18.4019 REMARK 3 T TENSOR REMARK 3 T11: 0.1423 T22: 0.1896 REMARK 3 T33: 0.3242 T12: -0.0537 REMARK 3 T13: -0.0078 T23: 0.0375 REMARK 3 L TENSOR REMARK 3 L11: 4.8472 L22: 3.3067 REMARK 3 L33: 3.3453 L12: -2.9861 REMARK 3 L13: 1.8932 L23: -0.9542 REMARK 3 S TENSOR REMARK 3 S11: -0.0415 S12: -0.3161 S13: -0.4977 REMARK 3 S21: -0.2156 S22: 0.0463 S23: 0.6933 REMARK 3 S31: 0.0922 S32: -0.3661 S33: -0.0048 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : BB 110 BB 125 REMARK 3 ORIGIN FOR THE GROUP (A): -11.2490 -16.0966 11.9725 REMARK 3 T TENSOR REMARK 3 T11: 0.3254 T22: 0.2020 REMARK 3 T33: 0.7015 T12: -0.0735 REMARK 3 T13: -0.1231 T23: -0.0554 REMARK 3 L TENSOR REMARK 3 L11: 12.0046 L22: 1.6903 REMARK 3 L33: 7.6274 L12: 1.5633 REMARK 3 L13: 3.4826 L23: -1.3020 REMARK 3 S TENSOR REMARK 3 S11: 0.0733 S12: -0.3773 S13: -1.4718 REMARK 3 S21: -0.3760 S22: 0.1285 S23: 0.4084 REMARK 3 S31: 0.5417 S32: -0.5917 S33: -0.2018 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7NKT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE. REMARK 100 THE DEPOSITION ID IS D_1292114165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9999 REMARK 200 MONOCHROMATOR : DCCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28115 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.297 REMARK 200 RESOLUTION RANGE LOW (A) : 46.103 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6Z1Z, 6XC4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM K2HPO4, 20% (W/V) PEG 8000, PH REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 64.04650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 64.04650 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.83800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.04650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.41900 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.04650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 58.25700 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 64.04650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.04650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 38.83800 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 64.04650 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 58.25700 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 64.04650 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 19.41900 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: AAA, BBB REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 319 REMARK 465 VAL A 320 REMARK 465 GLN A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 GLU A 324 REMARK 465 SER A 325 REMARK 465 ILE A 326 REMARK 465 VAL A 327 REMARK 465 ARG A 328 REMARK 465 PHE A 329 REMARK 465 PRO A 330 REMARK 465 ASN A 331 REMARK 465 LYS A 528 REMARK 465 LYS A 529 REMARK 465 SER A 530 REMARK 465 THR A 531 REMARK 465 ASN A 532 REMARK 465 LEU A 533 REMARK 465 VAL A 534 REMARK 465 LYS A 535 REMARK 465 ASN A 536 REMARK 465 LYS A 537 REMARK 465 CYS A 538 REMARK 465 VAL A 539 REMARK 465 ASN A 540 REMARK 465 PHE A 541 REMARK 465 HIS A 542 REMARK 465 HIS A 543 REMARK 465 HIS A 544 REMARK 465 HIS A 545 REMARK 465 HIS A 546 REMARK 465 HIS A 547 REMARK 465 GLU B 126 REMARK 465 GLN B 127 REMARK 465 LYS B 128 REMARK 465 LEU B 129 REMARK 465 ILE B 130 REMARK 465 SER B 131 REMARK 465 GLU B 132 REMARK 465 GLU B 133 REMARK 465 ASP B 134 REMARK 465 LEU B 135 REMARK 465 LYS B 136 REMARK 465 LYS B 137 REMARK 465 LYS B 138 REMARK 465 HIS B 139 REMARK 465 HIS B 140 REMARK 465 HIS B 141 REMARK 465 HIS B 142 REMARK 465 HIS B 143 REMARK 465 HIS B 144 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 CYS A 336 O REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHEAA 377 84.42 -150.36 REMARK 500 ASNAA 422 -54.97 -120.98 REMARK 500 PHEAA 429 127.47 -39.92 REMARK 500 HISAA 519 93.78 -60.39 REMARK 500 ALAAA 520 165.17 179.94 REMARK 500 SERBB 7 148.32 -173.38 REMARK 500 ALABB 91 166.47 179.68 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7B27 RELATED DB: PDB DBREF 7NKTAA 319 541 UNP P0DTC2 SPIKE_SARS2 319 541 DBREF 7NKTBB 1 144 PDB 7NKT 7NKT 1 144 SEQADV 7NKT HISAA 542 UNP P0DTC2 EXPRESSION TAG SEQADV 7NKT HISAA 543 UNP P0DTC2 EXPRESSION TAG SEQADV 7NKT HISAA 544 UNP P0DTC2 EXPRESSION TAG SEQADV 7NKT HISAA 545 UNP P0DTC2 EXPRESSION TAG SEQADV 7NKT HISAA 546 UNP P0DTC2 EXPRESSION TAG SEQADV 7NKT HISAA 547 UNP P0DTC2 EXPRESSION TAG SEQRES 1AA 229 ARG VAL GLN PRO THR GLU SER ILE VAL ARG PHE PRO ASN SEQRES 2AA 229 ILE THR ASN LEU CYS PRO PHE GLY GLU VAL PHE ASN ALA SEQRES 3AA 229 THR ARG PHE ALA SER VAL TYR ALA TRP ASN ARG LYS ARG SEQRES 4AA 229 ILE SER ASN CYS VAL ALA ASP TYR SER VAL LEU TYR ASN SEQRES 5AA 229 SER ALA SER PHE SER THR PHE LYS CYS TYR GLY VAL SER SEQRES 6AA 229 PRO THR LYS LEU ASN ASP LEU CYS PHE THR ASN VAL TYR SEQRES 7AA 229 ALA ASP SER PHE VAL ILE ARG GLY ASP GLU VAL ARG GLN SEQRES 8AA 229 ILE ALA PRO GLY GLN THR GLY LYS ILE ALA ASP TYR ASN SEQRES 9AA 229 TYR LYS LEU PRO ASP ASP PHE THR GLY CYS VAL ILE ALA SEQRES 10AA 229 TRP ASN SER ASN ASN LEU ASP SER LYS VAL GLY GLY ASN SEQRES 11AA 229 TYR ASN TYR LEU TYR ARG LEU PHE ARG LYS SER ASN LEU SEQRES 12AA 229 LYS PRO PHE GLU ARG ASP ILE SER THR GLU ILE TYR GLN SEQRES 13AA 229 ALA GLY SER THR PRO CYS ASN GLY VAL GLU GLY PHE ASN SEQRES 14AA 229 CYS TYR PHE PRO LEU GLN SER TYR GLY PHE GLN PRO THR SEQRES 15AA 229 ASN GLY VAL GLY TYR GLN PRO TYR ARG VAL VAL VAL LEU SEQRES 16AA 229 SER PHE GLU LEU LEU HIS ALA PRO ALA THR VAL CYS GLY SEQRES 17AA 229 PRO LYS LYS SER THR ASN LEU VAL LYS ASN LYS CYS VAL SEQRES 18AA 229 ASN PHE HIS HIS HIS HIS HIS HIS SEQRES 1BB 144 GLN VAL GLN LEU VAL GLU SER GLY GLY GLY SER VAL GLN SEQRES 2BB 144 PRO GLY GLY SER LEU ARG LEU SER CYS LEU GLY SER GLY SEQRES 3BB 144 SER LEU ASP TYR TYR ALA ILE GLY TRP PHE ARG GLN ALA SEQRES 4BB 144 PRO GLY LYS GLU ARG GLU GLY VAL SER CYS ILE ALA SER SEQRES 5BB 144 SER GLY ASP ARG THR ILE TYR ALA ASP SER VAL LYS GLY SEQRES 6BB 144 ARG PHE THR ILE SER ARG ASP TYR GLY LYS ASN THR VAL SEQRES 7BB 144 TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8BB 144 MET TYR TYR CYS ALA ALA LEU GLN GLY SER TYR TYR TYR SEQRES 9BB 144 THR GLY PHE VAL ALA ASN GLU TYR ASP TYR TRP GLY GLN SEQRES 10BB 144 GLY ALA PRO VAL THR VAL SER SER GLU GLN LYS LEU ILE SEQRES 11BB 144 SER GLU GLU ASP LEU LYS LYS LYS HIS HIS HIS HIS HIS SEQRES 12BB 144 HIS HET NAG AA 601 14 HET PO4 AA 602 5 HET PEG BB 201 7 HET PEG BB 202 7 HET PEG BB 203 7 HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM PO4 PHOSPHATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 3 NAG C8 H15 N O6 FORMUL 4 PO4 O4 P 3- FORMUL 5 PEG 3(C4 H10 O3) FORMUL 8 HOH *137(H2 O) HELIX 1 AA1 PROAA 337 ASNAA 343 1 7 HELIX 2 AA2 SERAA 349 TRPAA 353 5 5 HELIX 3 AA3 TYRAA 365 ASNAA 370 1 6 HELIX 4 AA4 LYSAA 386 ASPAA 389 5 4 HELIX 5 AA5 ASPAA 405 ILEAA 410 5 6 HELIX 6 AA6 GLYAA 416 ASNAA 422 1 7 HELIX 7 AA7 SERAA 438 SERAA 443 1 6 HELIX 8 AA8 GLYAA 502 TYRAA 505 5 4 HELIX 9 AA9 ASPBB 61 LYSBB 64 5 4 HELIX 10 AB1 LYSBB 86 THRBB 90 5 5 HELIX 11 AB2 VALBB 108 TYRBB 112 5 5 SHEET 1 AA1 5 ASNAA 354 ILEAA 358 0 SHEET 2 AA1 5 ASNAA 394 ARGAA 403 -1 O VALAA 395 N ILEAA 358 SHEET 3 AA1 5 PROAA 507 GLUAA 516 -1 O TYRAA 508 N ILEAA 402 SHEET 4 AA1 5 GLYAA 431 ASNAA 437 -1 N ILEAA 434 O VALAA 511 SHEET 5 AA1 5 THRAA 376 TYRAA 380 -1 N LYSAA 378 O VALAA 433 SHEET 1 AA2 3 CYSAA 361 VALAA 362 0 SHEET 2 AA2 3 VALAA 524 CYSAA 525 1 O CYSAA 525 N CYSAA 361 SHEET 3 AA2 3 CYSAA 391 PHEAA 392 -1 N PHEAA 392 O VALAA 524 SHEET 1 AA3 2 LEUAA 452 ARGAA 454 0 SHEET 2 AA3 2 LEUAA 492 SERAA 494 -1 O GLNAA 493 N TYRAA 453 SHEET 1 AA4 2 TYRAA 473 GLNAA 474 0 SHEET 2 AA4 2 CYSAA 488 TYRAA 489 -1 O TYRAA 489 N TYRAA 473 SHEET 1 AA5 4 LEUBB 4 SERBB 7 0 SHEET 2 AA5 4 LEUBB 18 GLYBB 24 -1 O LEUBB 23 N VALBB 5 SHEET 3 AA5 4 THRBB 77 METBB 82 -1 O METBB 82 N LEUBB 18 SHEET 4 AA5 4 PHEBB 67 ASPBB 72 -1 N THRBB 68 O GLNBB 81 SHEET 1 AA6 6 GLYBB 10 VALBB 12 0 SHEET 2 AA6 6 ALABB 119 VALBB 123 1 O THRBB 122 N GLYBB 10 SHEET 3 AA6 6 ALABB 91 LEUBB 98 -1 N TYRBB 93 O ALABB 119 SHEET 4 AA6 6 ALABB 32 GLNBB 38 -1 N GLYBB 34 O ALABB 96 SHEET 5 AA6 6 GLUBB 45 ILEBB 50 -1 O VALBB 47 N TRPBB 35 SHEET 6 AA6 6 THRBB 57 TYRBB 59 -1 O ILEBB 58 N CYSBB 49 SHEET 1 AA7 4 GLYBB 10 VALBB 12 0 SHEET 2 AA7 4 ALABB 119 VALBB 123 1 O THRBB 122 N GLYBB 10 SHEET 3 AA7 4 ALABB 91 LEUBB 98 -1 N TYRBB 93 O ALABB 119 SHEET 4 AA7 4 TYRBB 114 TRPBB 115 -1 O TYRBB 114 N ALABB 97 SSBOND 1 CYSAA 336 CYSAA 361 1555 1555 1.99 SSBOND 2 CYSAA 379 CYSAA 432 1555 1555 2.10 SSBOND 3 CYSAA 391 CYSAA 525 1555 1555 2.03 SSBOND 4 CYSAA 480 CYSAA 488 1555 1555 2.13 SSBOND 5 CYSBB 22 CYSBB 95 1555 1555 2.08 LINK ND2 ASNAA 343 C1 NAGAA 601 1555 1555 1.44 CRYST1 128.093 128.093 77.676 90.00 90.00 90.00 I 41 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.007807 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007807 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012874 0.00000