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PDBsum entry 1fqn

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Lyase PDB id
1fqn
Jmol
Contents
Protein chain
257 a.a. *
Waters ×135
* Residue conservation analysis
HEADER    LYASE                                   06-SEP-00   1FQN
TITLE     X-RAY CRYSTAL STRUCTURE OF METAL-FREE F93I/F95M/W97V
TITLE    2 CARBONIC ANHYDRASE (CAII) VARIANT
COMPND    MOL_ID: 1;
COMPND   2 MOLECULE: CARBONIC ANHYDRASE;
COMPND   3 CHAIN: A;
COMPND   4 EC: 4.2.1.1;
COMPND   5 ENGINEERED: YES;
COMPND   6 MUTATION: YES
SOURCE    MOL_ID: 1;
SOURCE   2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE   3 ORGANISM_COMMON: HUMAN;
SOURCE   4 ORGANISM_TAXID: 9606;
SOURCE   5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE   6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS    CARBONIC ANHYDRASE, METAL BINDING, METAL SPECIFICITY, LYASE
EXPDTA    X-RAY DIFFRACTION
AUTHOR    J.D.COX,J.A.HUNT,K.M.COMPHER,C.A.FIERKE,D.W.CHRISTIANSON
REVDAT   2   24-FEB-09 1FQN    1       VERSN
REVDAT   1   17-JAN-01 1FQN    0
JRNL        AUTH   J.D.COX,J.A.HUNT,K.M.COMPHER,C.A.FIERKE,
JRNL        AUTH 2 D.W.CHRISTIANSON
JRNL        TITL   STRUCTURAL INFLUENCE OF HYDROPHOBIC CORE RESIDUES
JRNL        TITL 2 ON METAL BINDING AND SPECIFICITY IN CARBONIC
JRNL        TITL 3 ANHYDRASE II.
JRNL        REF    BIOCHEMISTRY                  V.  39 13687 2000
JRNL        REFN                   ISSN 0006-2960
JRNL        PMID   11076507
JRNL        DOI    10.1021/BI001649J
REMARK   1
REMARK   2
REMARK   2 RESOLUTION.    2.00 ANGSTROMS.
REMARK   3
REMARK   3 REFINEMENT.
REMARK   3   PROGRAM     : X-PLOR 3.851
REMARK   3   AUTHORS     : BRUNGER
REMARK   3
REMARK   3  DATA USED IN REFINEMENT.
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : NULL
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : NULL
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : NULL
REMARK   3   NUMBER OF REFLECTIONS             : 16087
REMARK   3
REMARK   3  FIT TO DATA USED IN REFINEMENT.
REMARK   3   CROSS-VALIDATION METHOD          : NULL
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM
REMARK   3   R VALUE            (WORKING SET) : 0.189
REMARK   3   FREE R VALUE                     : 0.279
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : NULL
REMARK   3   FREE R VALUE TEST SET COUNT      : 785
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : NULL
REMARK   3
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.
REMARK   3   TOTAL NUMBER OF BINS USED           : NULL
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : NULL
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : NULL
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : NULL
REMARK   3   BIN R VALUE           (WORKING SET) : NULL
REMARK   3   BIN FREE R VALUE                    : NULL
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : NULL
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : NULL
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK   3
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK   3   PROTEIN ATOMS            : 2035
REMARK   3   NUCLEIC ACID ATOMS       : 0
REMARK   3   HETEROGEN ATOMS          : 0
REMARK   3   SOLVENT ATOMS            : 135
REMARK   3
REMARK   3  B VALUES.
REMARK   3   FROM WILSON PLOT           (A**2) : 17.80
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : NULL
REMARK   3   OVERALL ANISOTROPIC B VALUE.
REMARK   3    B11 (A**2) : NULL
REMARK   3    B22 (A**2) : NULL
REMARK   3    B33 (A**2) : NULL
REMARK   3    B12 (A**2) : NULL
REMARK   3    B13 (A**2) : NULL
REMARK   3    B23 (A**2) : NULL
REMARK   3
REMARK   3  ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM LUZZATI PLOT        (A) : NULL
REMARK   3   ESD FROM SIGMAA              (A) : NULL
REMARK   3   LOW RESOLUTION CUTOFF        (A) : NULL
REMARK   3
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : NULL
REMARK   3   ESD FROM C-V SIGMAA          (A) : NULL
REMARK   3
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.
REMARK   3   BOND LENGTHS                 (A) : NULL
REMARK   3   BOND ANGLES            (DEGREES) : 1.90
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : NULL
REMARK   3   IMPROPER ANGLES        (DEGREES) : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL MODEL : NULL
REMARK   3
REMARK   3  ISOTROPIC THERMAL FACTOR RESTRAINTS.    RMS    SIGMA
REMARK   3   MAIN-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   MAIN-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN BOND              (A**2) : NULL  ; NULL
REMARK   3   SIDE-CHAIN ANGLE             (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  NCS MODEL : NULL
REMARK   3
REMARK   3  NCS RESTRAINTS.                         RMS   SIGMA/WEIGHT
REMARK   3   GROUP  1  POSITIONAL            (A) : NULL  ; NULL
REMARK   3   GROUP  1  B-FACTOR           (A**2) : NULL  ; NULL
REMARK   3
REMARK   3  PARAMETER FILE  1  : NULL
REMARK   3  TOPOLOGY FILE  1   : NULL
REMARK   3
REMARK   3  OTHER REFINEMENT REMARKS: NULL
REMARK   4
REMARK   4 1FQN COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-00.
REMARK 100 THE RCSB ID CODE IS RCSB011826.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION
REMARK 200  DATE OF DATA COLLECTION        : 13-AUG-98
REMARK 200  TEMPERATURE           (KELVIN) : 130
REMARK 200  PH                             : 8.0
REMARK 200  NUMBER OF CRYSTALS USED        : 1
REMARK 200
REMARK 200  SYNCHROTRON              (Y/N) : N
REMARK 200  RADIATION SOURCE               : ROTATING ANODE
REMARK 200  BEAMLINE                       : NULL
REMARK 200  X-RAY GENERATOR MODEL          : RIGAKU
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M
REMARK 200  WAVELENGTH OR RANGE        (A) : 1.5418
REMARK 200  MONOCHROMATOR                  : NULL
REMARK 200  OPTICS                         : NULL
REMARK 200
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IIC
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK
REMARK 200
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 16220
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.000
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.3
REMARK 200  DATA REDUNDANCY                : 3.100
REMARK 200  R MERGE                    (I) : 0.06800
REMARK 200  R SYM                      (I) : NULL
REMARK 200   FOR THE DATA SET  : 8.4000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.07
REMARK 200  COMPLETENESS FOR SHELL     (%) : 94.0
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.60
REMARK 200  R MERGE FOR SHELL          (I) : 0.30900
REMARK 200  R SYM FOR SHELL            (I) : NULL
REMARK 200   FOR SHELL         : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS   (%): 40.38
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, PH 8.0,
REMARK 280  VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290      SYMOP   SYMMETRY
REMARK 290     NNNMMM   OPERATOR
REMARK 290       1555   X,Y,Z
REMARK 290       2555   -X,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       20.57000
REMARK 290   SMTRY3   2  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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER
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: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
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     MET A     1
REMARK 465     SER A     2
REMARK 465     HIS A     3
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3
REMARK 500    ARG A  27   NE  -  CZ  -  NH2 ANGL. DEV. =  -3.5 DEGREES
REMARK 500    LEU A  47   CA  -  CB  -  CG  ANGL. DEV. =  14.9 DEGREES
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    PRO A  21      -19.54    -48.90
REMARK 500    LYS A 111       -8.35     71.81
REMARK 500    PHE A 176       42.04   -143.21
REMARK 500    ASN A 244       56.50    -91.59
REMARK 500    LYS A 252     -134.87     62.81
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1FQL   RELATED DB: PDB
REMARK 900 ZINC-BOUND CARBONIC ANHYDRASE II (F95M/W97V) VARIANT.
REMARK 900 RELATED ID: 1FQM   RELATED DB: PDB
REMARK 900 ZINC-BOUND CARBONIC ANHYDRASE II (F93I/F95M/W97V) VARIANT.
REMARK 900 RELATED ID: 1FQR   RELATED DB: PDB
REMARK 900 COBALT-BOUND CARBONIC ANHYDRASE II (F93I/F95M/W97V) VARIANT.
REMARK 900 RELATED ID: 1FR4   RELATED DB: PDB
REMARK 900 COPPER-BOUND CARBONIC ANHYDRASE II (F93I/F95M/W97V) VARIANT.
REMARK 900 RELATED ID: 1FR7   RELATED DB: PDB
REMARK 900 ZINC-BOUND CARBONIC ANHYDRASE II (F93S/F95L/W97M) VARIANT.
DBREF  1FQN A    1   261  UNP    P00918   CAH2_HUMAN       1    260
SEQADV 1FQN ILE A   93  UNP  P00918    PHE    92 ENGINEERED
SEQADV 1FQN MET A   95  UNP  P00918    PHE    94 ENGINEERED
SEQADV 1FQN VAL A   97  UNP  P00918    TRP    96 ENGINEERED
SEQRES   1 A  260  MET SER HIS HIS TRP GLY TYR GLY LYS HIS ASN GLY PRO
SEQRES   2 A  260  GLU HIS TRP HIS LYS ASP PHE PRO ILE ALA LYS GLY GLU
SEQRES   3 A  260  ARG GLN SER PRO VAL ASP ILE ASP THR HIS THR ALA LYS
SEQRES   4 A  260  TYR ASP PRO SER LEU LYS PRO LEU SER VAL SER TYR ASP
SEQRES   5 A  260  GLN ALA THR SER LEU ARG ILE LEU ASN ASN GLY HIS ALA
SEQRES   6 A  260  PHE ASN VAL GLU PHE ASP ASP SER GLN ASP LYS ALA VAL
SEQRES   7 A  260  LEU LYS GLY GLY PRO LEU ASP GLY THR TYR ARG LEU ILE
SEQRES   8 A  260  GLN ILE HIS MET HIS VAL GLY SER LEU ASP GLY GLN GLY
SEQRES   9 A  260  SER GLU HIS THR VAL ASP LYS LYS LYS TYR ALA ALA GLU
SEQRES  10 A  260  LEU HIS LEU VAL HIS TRP ASN THR LYS TYR GLY ASP PHE
SEQRES  11 A  260  GLY LYS ALA VAL GLN GLN PRO ASP GLY LEU ALA VAL LEU
SEQRES  12 A  260  GLY ILE PHE LEU LYS VAL GLY SER ALA LYS PRO GLY LEU
SEQRES  13 A  260  GLN LYS VAL VAL ASP VAL LEU ASP SER ILE LYS THR LYS
SEQRES  14 A  260  GLY LYS SER ALA ASP PHE THR ASN PHE ASP PRO ARG GLY
SEQRES  15 A  260  LEU LEU PRO GLU SER LEU ASP TYR TRP THR TYR PRO GLY
SEQRES  16 A  260  SER LEU THR THR PRO PRO LEU LEU GLU CYS VAL THR TRP
SEQRES  17 A  260  ILE VAL LEU LYS GLU PRO ILE SER VAL SER SER GLU GLN
SEQRES  18 A  260  VAL LEU LYS PHE ARG LYS LEU ASN PHE ASN GLY GLU GLY
SEQRES  19 A  260  GLU PRO GLU GLU LEU MET VAL ASP ASN TRP ARG PRO ALA
SEQRES  20 A  260  GLN PRO LEU LYS ASN ARG GLN ILE LYS ALA SER PHE LYS
FORMUL   2  HOH   *135(H2 O)
HELIX    1   1 HIS A   15  PHE A   20  1                                   6
HELIX    2   2 PRO A   21  GLY A   25  5                                   5
HELIX    3   3 LYS A  127  GLY A  129  5                                   3
HELIX    4   4 ASP A  130  VAL A  135  1                                   6
HELIX    5   5 LYS A  154  ASP A  162  1                                   9
HELIX    6   6 VAL A  163  LYS A  168  5                                   6
HELIX    7   7 ASP A  180  LEU A  185  5                                   6
HELIX    8   8 SER A  219  ARG A  227  1                                   9
SHEET    1   A 2 ASP A  32  ILE A  33  0
SHEET    2   A 2 THR A 108  VAL A 109  1  O  THR A 108   N  ILE A  33
SHEET    1   B16 SER A 173  ASP A 175  0
SHEET    2   B16 SER A  56  ASN A  61 -1  N  ILE A  59   O  ALA A 174
SHEET    3   B16 PHE A  66  PHE A  70 -1  N  ASN A  67   O  LEU A  60
SHEET    4   B16 TYR A  88  VAL A  97 -1  O  ILE A  91   N  PHE A  70
SHEET    5   B16 VAL A  78  GLY A  81 -1  N  LEU A  79   O  TYR A  88
SHEET    6   B16 LEU A  47  SER A  50 -1  N  SER A  48   O  LYS A  80
SHEET    7   B16 VAL A  78  GLY A  81 -1  O  VAL A  78   N  SER A  50
SHEET    8   B16 TYR A  88  VAL A  97 -1  O  TYR A  88   N  LEU A  79
SHEET    9   B16 ALA A 116  ASN A 124 -1  O  GLU A 117   N  HIS A  96
SHEET   10   B16 LEU A 141  VAL A 150 -1  N  ALA A 142   O  HIS A 122
SHEET   11   B16 ILE A 216  VAL A 218  1  N  ILE A 216   O  PHE A 147
SHEET   12   B16 LEU A 141  VAL A 150  1  O  PHE A 147   N  ILE A 216
SHEET   13   B16 VAL A 207  LEU A 212  1  N  THR A 208   O  LEU A 141
SHEET   14   B16 TYR A 191  GLY A 196 -1  O  TRP A 192   N  VAL A 211
SHEET   15   B16 LYS A 257  ALA A 258 -1  N  LYS A 257   O  THR A 193
SHEET   16   B16 LYS A  39  TYR A  40  1  O  LYS A  39   N  ALA A 258
CISPEP   1 SER A   29    PRO A   30          0        -0.03
CISPEP   2 PRO A  201    PRO A  202          0         0.38
CRYST1   41.700   41.140   71.980  90.00 102.91  90.00 P 1 21 1      2
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      0.023981  0.000000  0.005497        0.00000
SCALE2      0.000000  0.024307  0.000000        0.00000
SCALE3      0.000000  0.000000  0.014253        0.00000
      
PROCHECK
Go to PROCHECK summary
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