REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7_650) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 30850 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1567 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.5818 - 6.8861 0.99 2710 163 0.2199 0.2326 REMARK 3 2 6.8861 - 5.4691 1.00 2689 142 0.2584 0.2998 REMARK 3 3 5.4691 - 4.7788 1.00 2679 150 0.2146 0.2478 REMARK 3 4 4.7788 - 4.3423 1.00 2668 131 0.2048 0.2750 REMARK 3 5 4.3423 - 4.0313 1.00 2660 147 0.2287 0.3163 REMARK 3 6 4.0313 - 3.7938 1.00 2663 143 0.2441 0.3429 REMARK 3 7 3.7938 - 3.6039 1.00 2645 136 0.2588 0.3516 REMARK 3 8 3.6039 - 3.4470 1.00 2668 132 0.2629 0.3130 REMARK 3 9 3.4470 - 3.3144 1.00 2644 141 0.2858 0.3557 REMARK 3 10 3.3144 - 3.2001 1.00 2614 152 0.3221 0.3564 REMARK 3 11 3.2001 - 3.1000 0.99 2643 130 0.3493 0.4033 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.83 REMARK 3 K_SOL : 0.29 REMARK 3 B_SOL : 77.33 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.450 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 105.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -17.85780 REMARK 3 B22 (A**2) : 5.96060 REMARK 3 B33 (A**2) : 11.89720 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : -8.78940 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.017 11517 REMARK 3 ANGLE : 1.507 15184 REMARK 3 CHIRALITY : 0.096 1775 REMARK 3 PLANARITY : 0.008 1897 REMARK 3 DIHEDRAL : 21.569 4189 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4JM2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-APR-13. REMARK 100 THE RCSB ID CODE IS RCSB078216. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : LIQUID N2 COOLED DOUBLE CRYSTAL REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30862 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 43.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.60000 REMARK 200 FOR SHELL : 1.900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG2000, 0.1 M TRIS, PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 109.20450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.07300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 109.20450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.07300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: HEXAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 SER A 127 REMARK 465 SER A 128 REMARK 465 LYS A 129 REMARK 465 SER A 130 REMARK 465 THR A 131 REMARK 465 SER A 132 REMARK 465 GLY A 133 REMARK 465 SER A 215 REMARK 465 CYS A 216 REMARK 465 LYS D 129 REMARK 465 SER D 130 REMARK 465 THR D 131 REMARK 465 SER D 132 REMARK 465 GLY D 133 REMARK 465 GLY D 134 REMARK 465 THR D 135 REMARK 465 ALA D 136 REMARK 465 ALA D 137 REMARK 465 ARG E 318 REMARK 465 PRO E 319 REMARK 465 GLY E 320 REMARK 465 GLU E 321 REMARK 465 ILE E 322 REMARK 465 GLU E 492 REMARK 465 VAL F 176 REMARK 465 LEU F 177 REMARK 465 ALA F 178 REMARK 465 PHE F 179 REMARK 465 GLN F 180 REMARK 465 LYS F 181 REMARK 465 ALA F 182 REMARK 465 SER F 183 REMARK 465 ASN F 184 REMARK 465 THR F 185 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 ND2 ASN E 386 O5 NAG E 519 1.81 REMARK 500 SG CYS D 140 CB CYS D 196 1.89 REMARK 500 O6 MAN E 512 O5 MAN E 513 1.97 REMARK 500 O4 NAG E 510 C2 BMA E 511 1.99 REMARK 500 O3 BMA E 503 O5 MAN E 507 2.07 REMARK 500 O6 MAN E 504 O5 MAN E 505 2.09 REMARK 500 SG CYS F 130 CB CYS F 159 2.12 REMARK 500 ND2 ASN E 362 C2 NAG E 523 2.16 REMARK 500 C3 BMA E 503 C1 MAN E 507 2.16 REMARK 500 CG ASN E 448 C1 NAG E 524 2.18 REMARK 500 O6 BMA E 503 O5 MAN E 504 2.18 REMARK 500 ND2 ASN E 262 C2 NAG E 522 2.18 REMARK 500 ND2 ASN E 448 C2 NAG E 524 2.18 REMARK 500 O4 NAG E 510 O5 BMA E 511 2.19 REMARK 500 CG ASN E 332 C1 NAG E 501 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 15 -6.32 88.05 REMARK 500 ASP A 27 -171.21 -173.72 REMARK 500 TRP A 34 23.79 82.03 REMARK 500 LYS A 35B 67.02 62.20 REMARK 500 ARG A 54 8.73 -68.58 REMARK 500 SER A 62 -16.15 -44.36 REMARK 500 SER A 82B 43.75 36.76 REMARK 500 ARG A 96 -155.57 -147.21 REMARK 500 HIS A 97 -164.57 -171.04 REMARK 500 ASP A 144 63.47 65.19 REMARK 500 ASN A 204 70.75 61.50 REMARK 500 ILE B 29 15.75 -143.09 REMARK 500 ASN B 30 -131.06 53.87 REMARK 500 THR B 51 -58.94 71.64 REMARK 500 SER B 65 171.39 177.25 REMARK 500 ASN B 77 71.97 39.50 REMARK 500 MET B 78 142.43 -39.43 REMARK 500 ALA B 84 -179.80 -170.94 REMARK 500 TYR B 91 51.79 -140.58 REMARK 500 PRO B 113 -169.02 -69.06 REMARK 500 SER C 30 -120.19 51.39 REMARK 500 ALA C 51 -58.36 72.89 REMARK 500 ALA C 84 -173.18 -170.80 REMARK 500 ASN C 152 -3.07 77.61 REMARK 500 ASN D 82B 96.30 81.85 REMARK 500 GLN E 258 -62.81 69.53 REMARK 500 GLU E 268 -131.88 61.90 REMARK 500 PRO E 299 -165.10 -59.47 REMARK 500 ILE E 326 -151.56 170.95 REMARK 500 ALA E 329 -168.25 -122.35 REMARK 500 ASN E 392 63.83 -156.34 REMARK 500 ASN E 407 50.89 162.75 REMARK 500 GLU E 409 173.27 178.12 REMARK 500 ASN E 461 -45.53 -130.36 REMARK 500 LYS E 485 31.41 -98.72 REMARK 500 LYS F 2 130.45 -38.05 REMARK 500 ILE F 36 -60.01 -95.61 REMARK 500 SER F 57 -168.05 -124.50 REMARK 500 ASN F 73 61.08 35.83 REMARK 500 ASP F 105 -177.61 -171.76 REMARK 500 THR F 106 -1.28 81.39 REMARK 500 ILE F 174 134.25 -173.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG E 522 BOUND REMARK 800 TO ASN E 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG E 526 BOUND REMARK 800 TO ASN E 276 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG E 527 BOUND REMARK 800 TO ASN E 295 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E REMARK 800 332 RESIDUES 501 TO 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG E 525 BOUND REMARK 800 TO ASN E 339 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG E 523 BOUND REMARK 800 TO ASN E 362 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E REMARK 800 386 RESIDUES 519 TO 521 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN E OF SUGAR BOUND TO ASN E REMARK 800 392 RESIDUES 509 TO 518 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR MONO-SACCHARIDE NAG E 524 BOUND REMARK 800 TO ASN E 448 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JM4 RELATED DB: PDB REMARK 900 STRUCTURE OF UNLIGANDED PGT 135 FAB