Protein Data Bank Changes Guide. New Changes in Version 3.20 September 15, 2008
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1 New Records in 3.2 Page 1 Protein Data Bank Changes Guide New Changes in Version 3.20 September 15, 2008 Version 3.20 of the PDB file format introduces a small number of changes and extensions supporting the annotation practices adopted by the wwpdb. These annotation practices are described in detail in the documentation section of the wwpdb website. The complete details of the PDB file format can be found at
2 New Records in 3.2 Page 2 1. SPLIT When a structure has too many atoms to be represented in a single PDB formatted file, it will be split into smaller entries that will all be identified with a new record named SPLIT. Appears after TITLE. SPLIT 1VOQ 1VOR 1VOS 1VOU 1VOV 1VOW 1VOX 1VOY SPLIT 2 1VP0 1VOZ HEADER RIBOSOME 06-OCT-04 1VOV TITLE CRYSTAL STRUCTURE OF FIVE 70S RIBOSOMES FROM ESCHERICHIA TITLE 2 COLI IN COMPLEX WITH PROTEIN Y. THIS FILE CONTAINS THE 30S TITLE 3 SUBUNIT OF ONE 70S RIBOSOME. SPLIT 1VOQ 1VOR 1VOS 1VOU 1VOV 1VOW 1VOX 1VOY 1VOZ SPLIT 2 1VP0 1VOZ 2. COMPND An additional column will be added to extend the continuation lines up to 999. COMPND 97 MOL_ID: 25; COMPND 98 MOLECULE: 50S RIBOSOMAL PROTEIN L32E; COMPND 99 CHAIN: Y; COMPND 100 SYNONYM: HL5; COMPND 101 MOL_ID: 26; COMPND 102 MOLECULE: 50S RIBOSOMAL PROTEIN L37AE; COMPND 103 CHAIN: Z; COMPND 104 MOL_ID: 27; COMPND 105 MOLECULE: 50S RIBOSOMAL PROTEIN L37E; COMPND 106 CHAIN: 1; COMPND 107 SYNONYM: L35E; 3. SOURCE The NCBI Taxonomy IDs for the organism (ORGANISM_TAXID) and expression system (EXPRESSION_SYSTEM_TAXID) are now included in the SOURCE record if they are available. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS CASEI; SOURCE 4 ORGANISM_TAXID: 1582; SOURCE 5 GENE: THYA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 SOURCE 9 EXPRESSION_SYSTEM_STRAIN: CHI2913RECA; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PSCTS9
3 New Records in 3.2 Page 3 An additional column will be added to extend the continuation lines up to 999. SOURCE 99 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 100 MOL_ID: 29; SOURCE 101 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 102 MOL_ID: 30; SOURCE 103 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 104 MOL_ID: 31; SOURCE 105 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; 4. EXPDTA The experimental methods have been standardized and follow an enumeration list. Multiple exp methods will be listed here for joint refinement or hybrid methods. NMR entries will be identified by solution and solid state. EM entries will be identified by electron crystallography and electron microscopy. X-RAY DIFFRACTION NEUTRON DIFFRACTION FIBER DIFFRACTION ELECTRON CRYSTALLOGRAPHY ELECTRON MICROSCOPY SOLUTION NMR SOLID-STATE NMR SOLUTION SCATTERING Example 1: EXPDTA SOLID-STATE NMR Example 2, joint refinement: EXPDTA X-RAY DIFFRACTION; NEUTRON DIFFRACTION 5. NUMMDL The new record NUMMDL specifies the number of models. Appears after EXPDTA. Example, ensemble without minimized average: EXPDTA SOLUTION NMR NUMMDL MDLTYP The new record MDLTYP specifies the minimized average or Ca/P atoms chains. Appears after EXPDTA with continuous lines. Example 1, only one minimized average: EXPDTA SOLUTION NMR MDLTYP MINIMIZED AVERAGE
4 New Records in 3.2 Page 4 Example 2, chains contain Ca or P atoms only: MDLTYP CA ATOMS ONLY, CHAIN A, B, C, D, E, F, G, H, I, J, K; P ATOMS ONLY, MDLTYP 2 CHAIN X, Y, Z Example 3, minimized average AND chains contain Ca or P atoms only: MDLTYP MINIMIZED AVERAGE; CA ATOMS ONLY, CHAIN A, B 7. JRNL Country code, ASTM and ISBN have been removed. The PubMed ID and corresponding Digital Object Identifier (DOI) for the primary citation have been added. Each DOI consists of a publisher prefix, a slash ("/"), and a suffix of numbers and letters of any length. The PubMed ID and DOI start at column 20. JRNL REF PROC.NATL.ACAD.SCI.USA V JRNL REFN ISSN JRNL PMID JRNL DOI /pnas REMARK 2 Format has been changed to allow display of low resolution. Resolution becomes f7.2 to allow for space and ANGSTROM. REMARK 2 RESOLUTION ANGSTROMS. 9. REMARK 4 The versioning now has format x.xx with uniform date format dd-mmm-yy. REMARK 4 2G86 COMPLIES WITH FORMAT V. 3.20, 01-AUG REMARK 100 For entries processed at RCSB, PDBE, or PDBJ, this remark indicates the data processing site, processing date with uniform format dd-mmm-yy, and site ID code. For entries processed at BNL, this record will only include the data processing site. Examples: REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB on 10-MAR-06. REMARK 100 THE RCSB ID CODE IS RCSB REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE on 13-FEB-07. REMARK 100 THE PDBE ID CODE IS EBI REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ on 21-MAR-05.
5 New Records in 3.2 Page 5 REMARK 100 THE RCSB ID CODE IS RCSB REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. 11. REMARK 200 This remark will have the uniform date format dd-mmm-yy. REMARK 200 DATE OF DATA COLLECTION : 01-JAN REMARK 240 This remark is mandatory for ELECTRON CRYSTALLOGRAPHY. Three new records have been added: RECONSTRUCTION METHOD, SAMPLE TYPE, and SPECIMEN TYPE. The DATE OF DATA COLLECTION will have the uniform date format dd-mmm-yy. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 2D CRYSTAL REMARK 240 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 240 DATA AQUISITION REMARK 240 DATE OF DATA COLLECTION : 01-DEC-03 REMARK 240 TEMPERATURE (KELVIN) : REMARK 240 PH : 6.00 REMARK 240 NUMBER OF CRYSTALS USED : 286 REMARK 240 MICROSCOPE MODEL : JEM3000SFF REMARK 240 DETECTOR TYPE : CCD REMARK 240 ACCELERATION VOLTAGE (KV) : 300 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : REMARK 240 RESOLUTION RANGE HIGH (A) : 1.9 REMARK 240 RESOLUTION RANGE LOW (A) : REMARK 240 DATA SCALING SOFTWARE : SOFTWARE REMARK 240 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 240 DATA REDUNDANCY : REMARK 240 IN THE HIGHEST RESOLUTION SHELL. REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.0 REMARK 240 COMPLETENESS FOR SHELL (%) : 82.0 REMARK 240 DATA REDUNDANCY IN SHELL : 5.70 REMARK 240 R MERGE FOR SHELL (I) : REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REMARK 240 REPLACEMENT REMARK 240 SOFTWARE USED : CNS REMARK 240 STARTING MODEL : PDB ENTRY 1SOR
6 New Records in 3.2 Page REMARK 245 This remark is mandatory for ELECTRON MICROSCOPY. Four new PDB records have been added: RECONSTRUCTION METHOD, SAMPLE TYPE, SPECIMEN TYPE, and PARTICLE TYPE if SAMPLE TYPE is PARTICLE. The DATE OF EXPERIMENT will have the uniform date format dd-mmm-yy. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : VITREOUS ICE (CRYO EM) REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : MIXED SYMMETRY REMARK 245 NAME OF SAMPLE : BACTERIOPHAGE T4 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : H2O REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : PHAGE REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : 06-JAN-02 REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : REMARK 245 MICROSCOPE MODEL : FEI/PHILIPS CM300FEG/T REMARK 245 DETECTOR TYPE : NULL REMARK 245 MINIMUM DEFOCUS (NM) : REMARK 245 MAXIMUM DEFOCUS (NM) : REMARK 245 MINIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : 0.00 REMARK 245 NOMINAL CS : 1.40 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : REMARK 245 ILLUMINATION MODE : SPOT SCAN REMARK 245 NOMINAL MAGNIFICATION : REMARK 245 CALIBRATED MAGNIFICATION : REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL The point symmetry will be in the last line of THE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR 00 CYCLIC POINT SYMMETRY (SCHOENFLIES SYMBOL = C38).
7 New Records in 3.2 Page In SPLIT entries, 50 reports the quaternary structure for the partial structure. Surface area is not reported. Example, SPLIT entries: 50 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN 50 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE 50 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS 50 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND 50 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN BIOMOLECULE: 1 50 QUATERNARY STRUCTURE FOR THIS ENTRY: 21MERIC 50 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, 50 AND CHAINS: J, K, L, M, N, O, P, Q, R, 50 AND CHAINS: S, T, a 50 BIOMT BIOMT BIOMT In non-split entries, 50 reports the full quaternary structure and softwarecalculated outputs, if available. Example, non-split entries: 50 BIOMOLECULE: 1 50 AUTHOR DETERMINED BIOLOGICAL UNIT: DODECAMERIC 50 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC 50 SOFTWARE USED: PISA 50 TOTAL BURIED SURFACE AREA: 2990 ANGSTROM**2 50 SURFACE AREA OF THE COMPLEX: 9330 ANGSTROM**2 50 CHANGE IN SOLVENT FREE ENERGY: KCAL/MOL 50 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, 50 AND CHAINS: J, K, L 50 BIOMT BIOMT BIOMT REMARK 465 For NMR ensembles, the missing residues will be listed in model range. REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 2
8 New Records in 3.2 Page REMARK 470 For NMR ensembles, the missing atoms will be listed in model range. REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-25 REMARK 470 RES CSSEQI ATOMS REMARK 470 ILE A 20 CD1 REMARK 470 THR A 59 CG2 18. REMARK 800 REMARK 800 will distinguish between author-provided and software-generated SITE records with an EVIDENCE CODE where the value can be AUTHOR/SOFTWARE/UNKNOWN. This appears after SITE_IDENTIFIER. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BIL A 19 REMARK 800 REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: DESIGNATED RECOGNITION REGION IN PRIMARY REMARK 800 REFERENCE. PROPOSED TO AFFECT SUBSTRATE SPECIFICITY.
9 New Records in 3.2 Page DBREF, DBREF1, and DBREF2 The DBREF record provides cross-reference links between PDB sequences and the corresponding database entry or entries in a given, fixed character space. This record will continue to be used as long as an accession code fits in the space provided (e.g., UNP code). Two new DBREF records (DBREF1 and DBREF2) will only be used when the accession code or sequence numbering does not fit to DBREF format such as (e.g., UNIMES or GB). Example, DBREF: DBREF 2J83 A UNP Q8TL28 Q8TL28_METAC In the new format, 20 characters are reserved for accession code and 10 characters are reserved for DB numbering. Example, DBREF1 and DBREF2: DBREF1 2J83 A UNIMES UPI000148A153 DBREF2 2J83 A MES DBREF1 2J83 A GB AE DBREF2 2J83 A All entries will self-reference if a database sequence is not available. Example, No Database Sequence: DBREF 2JSK A 1 23 PDB 2JSK 2JSK REMARK 630, Peptide inhibitors New record REMARK 630 describes the chemistry, function, or structure features for any antibiotics, inhibitors or peptide inhibitors that are treated as single molecules. Template: REMARK 630 MOLECULE TYPE: REMARK 630 MOLECULE NAME: REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 SOURCE: REMARK 630 SUBCOMP: REMARK 630 STRUCTURE DETAILS: REMARK 630 OTHER DETAILS: 21. for Phenix template/example and joint refinement for X-ray/Neutron Phenix templates have been added to. Example, PHENIX:
10 New Records in 3.2 Page 10 REFINEMENT. PROGRAM : PHENIX (PHENIX.REFINE) AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN : DAVIS,KRESHNA GOPAL,RALF GROSSE- : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL : MORIARTY,REETAL PAI,RANDY READ,JANE : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, : LAURENT STORONI,TOM TERWILLIGER,PETER : ZWART REFINEMENT TARGET : ML DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH (ANGSTROMS) : 2.99 RESOLUTION RANGE LOW (ANGSTROMS) : MIN(FOBS/SIGMA_FOBS) : COMPLETENESS FOR RANGE (%) : 96.7 NUMBER OF REFLECTIONS : FIT TO DATA USED IN REFINEMENT. R VALUE (WORKING + TEST SET) : R VALUE (WORKING SET) : FREE R VALUE : FREE R VALUE TEST SET SIZE (%) : FREE R VALUE TEST SET COUNT : FIT TO DATA USED IN REFINEMENT (IN BINS). BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE BULK SOLVENT MODELLING.
11 New Records in 3.2 Page 11 METHOD USED : FLAT BULK SOLVENT MODEL SOLVENT RADIUS : 1.11 SHRINKAGE RADIUS : 0.90 K_SOL : 0.30 B_SOL : ERROR ESTIMATES. COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : B VALUES. FROM WILSON PLOT (A**2) : MEAN B VALUE (OVERALL, A**2) : OVERALL ANISOTROPIC B VALUE. B11 (A**2) : B22 (A**2) : B33 (A**2) : B12 (A**2) : B13 (A**2) : B23 (A**2) : TWINNING INFORMATION. FRACTION: NULL OPERATOR: NULL DEVIATIONS FROM IDEAL VALUES. RMSD COUNT BOND : ANGLE : CHIRALITY : PLANARITY : DIHEDRAL : TLS DETAILS NUMBER OF TLS GROUPS : 2 TLS GROUP : 1 SELECTION: CHAIN A ORIGIN FOR THE GROUP (A): T TENSOR T11: T22: T33: T12: T13: T23: L TENSOR L11: L22: L33: L12: L13: L23: S TENSOR S11: S12: S13: S21: S22: S23: S31: S32: S33: TLS GROUP : 2 SELECTION: CHAIN B ORIGIN FOR THE GROUP (A): T TENSOR T11: T22: T33: T12: T13: T23: L TENSOR L11: L22: L33: L12: L13: L23: S TENSOR
12 New Records in 3.2 Page 12 S11: S12: S13: S21: S22: S23: S31: S32: S33: NCS DETAILS NUMBER OF NCS GROUPS : 3 NCS GROUP : 1 NCS OPERATOR : 1 REFERENCE SELECTION: CHAIN A AND (RESSEQ 2:525 ) SELECTION : CHAIN B AND (RESSEQ 2:525 ) ATOM PAIRS NUMBER : 3856 RMSD : NCS OPERATOR : 2 REFERENCE SELECTION: CHAIN A AND (RESSEQ 2:525 ) SELECTION : CHAIN C AND (RESSEQ 2:525 ) ATOM PAIRS NUMBER : 3856 RMSD : NCS GROUP : 2 NCS OPERATOR : 1 REFERENCE SELECTION: CHAIN H AND (RESSEQ 2:525 ) SELECTION : CHAIN I AND (RESSEQ 2:525 ) ATOM PAIRS NUMBER : 3856 RMSD : NCS OPERATOR : 2 REFERENCE SELECTION: CHAIN H AND (RESSEQ 2:525 ) SELECTION : CHAIN J AND (RESSEQ 2:525 ) ATOM PAIRS NUMBER : 3856 RMSD : NCS GROUP : 3 NCS OPERATOR : 1 REFERENCE SELECTION: CHAIN O AND (RESSEQ 1:97 ) SELECTION : CHAIN P AND (RESSEQ 1:97 ) ATOM PAIRS NUMBER : 728 RMSD : NCS OPERATOR : 2 REFERENCE SELECTION: CHAIN O AND (RESSEQ 1:97 ) SELECTION : CHAIN Q AND (RESSEQ 1:97 ) ATOM PAIRS NUMBER : 728 RMSD : OTHER REFINEMENT REMARKS: NULL Example, PHENIX X-ray/neutron joint refinement: REFINEMENT. PROGRAM : PHENIX (PHENIX.REFINE) AUTHORS : PAUL ADAMS, PAVEL AFONINE, VICENT CHEN, IAN : DAVIS, KRESHNA GOPAL, RALF GROSSE-KUNSTLEVE, : LI-WEI HUNG, ROBERT IMMORMINO, TOM IOERGER, : AIRLIE MCCOY, ERIK MCKEE, NIGEL MORIARTY, : REETAL PAI, RANDY READ, JANE RICHARDSON, : DAVID RICHARDSON, TOD ROMO, JIM : SACCHETTINI, NICHOLAS SAUTER, JACOB SMITH, : LAURENT STORONI, TOM TERWILLIGER, PETER : ZWART X-RAY DATA. REFINEMENT TARGET : ML
13 New Records in 3.2 Page 13 DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH (ANGSTROMS) : RESOLUTION RANGE LOW (ANGSTROMS) : MIN(FOBS/SIGMA_FOBS) : 1.33 COMPLETENESS FOR RANGE (%) : NUMBER OF REFLECTIONS : FIT TO DATA USED IN REFINEMENT. R VALUE (WORKING + TEST SET) : R VALUE (WORKING SET) : FREE R VALUE : FREE R VALUE TEST SET SIZE (%) : 9.36 FREE R VALUE TEST SET COUNT : 2952 FIT TO DATA USED IN REFINEMENT (IN BINS). BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE BULK SOLVENT MODELLING. METHOD USED : FLAT BULK SOLVENT MODEL SOLVENT RADIUS : 1.11 SHRINKAGE RADIUS : 0.90 GRID STEP FACTOR : 4.00 K_SOL : B_SOL : ERROR ESTIMATES. COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.19 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : OVERALL SCALE FACTORS. SCALE = SUM( F_OBS * F_MODEL )/SUM( F_MODEL **2) : ANISOTROPIC SCALE MATRIX ELEMENTS (IN CARTESIAN BASIS). B11 : B22 : B33 : B12 : B13 : B23 : NEUTRON DATA.
14 New Records in 3.2 Page 14 REFINEMENT TARGET : ML DATA USED IN REFINEMENT. RESOLUTION RANGE HIGH (ANGSTROMS) : RESOLUTION RANGE LOW (ANGSTROMS) : MIN(FOBS/SIGMA_FOBS) : 1.53 COMPLETENESS FOR RANGE (%) : NUMBER OF REFLECTIONS : FIT TO DATA USED IN REFINEMENT. R VALUE (WORKING + TEST SET) : R VALUE (WORKING SET) : FREE R VALUE : FREE R VALUE TEST SET SIZE (%) : 8.35 FREE R VALUE TEST SET COUNT : 992 FIT TO DATA USED IN REFINEMENT (IN BINS). BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE BULK SOLVENT MODELLING. METHOD USED : FLAT BULK SOLVENT MODEL SOLVENT RADIUS : 1.11 SHRINKAGE RADIUS : 0.90 GRID STEP FACTOR : 4.00 K_SOL : B_SOL : ERROR ESTIMATES. COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.45 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : OVERALL SCALE FACTORS. SCALE = SUM( F_OBS * F_MODEL )/SUM( F_MODEL **2) : ANISOTROPIC SCALE MATRIX ELEMENTS (IN CARTESIAN BASIS). B11 : B22 : B33 : B12 : B13 : B23 : MODEL CONTENT. ELEMENT ATOM RECORD COUNT OCCUPANCY SUM C D F O N P S Br TOTAL DEVIATIONS FROM IDEAL VALUES. RMSD MAX COUNT
15 New Records in 3.2 Page 15 BOND : ANGLE : CHIRALITY : PLANARITY : DIHEDRAL : MIN NONBONDED DISTANCE : DEVIATIONS FROM IDEAL VALUES (HISTOGRAM). BONDS ANGLES NONBONDED ATOMIC DISPLACEMENT PARAMETERS. WILSON B : ATOMS NUMBER OF ATOMS ISOTROPIC OR EQUIVALENT ISO. ANISO. MIN MAX MEAN ALL : ALL (NO H) : SOLVENT : NON-SOLVENT : HYDROGENS : ATOMIC DISPLACEMENT PARAMETERS (HISTOGRAM, NON-H). ISOTROPIC OR EQUIVALENT
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