HEADER    DNA                                     22-SEP-14   4RE7              
TITLE     LAMBDA-[RU(TAP)2(DPPZ)]2+ BOUND TO D(TCIGCGCCGA)                      
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-D(*TP*CP*IP*GP*CP*GP*CP*CP*GP*A)-3';                    
COMPND   3 CHAIN: A;                                                            
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;                            
SOURCE   4 ORGANISM_TAXID: 32630                                                
KEYWDS    INOSINE, KINKING, RUTHENIUM, DNA                                      
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    J.P.HALL,C.J.CARDIN                                                   
REVDAT   3   28-FEB-24 4RE7    1       REMARK LINK                              
REVDAT   2   22-NOV-17 4RE7    1       REMARK                                   
REVDAT   1   30-SEP-15 4RE7    0                                                
JRNL        AUTH   J.P.HALL,S.P.GURUNG,H.BEER,K.BUCHNER,D.J.CARDIN,J.A.BRAZIER, 
JRNL        AUTH 2 C.J.CARDIN                                                   
JRNL        TITL   THE EFFECTS OF DNA MODIFICATION ON THE BINDING OF            
JRNL        TITL 2 POLYPYRIDYL RUTHENIUM COMPLEXES                              
JRNL        REF    TO BE PUBLISHED                                              
JRNL        REFN                                                                
REMARK   2                                                                      
REMARK   2 RESOLUTION.    2.18 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : PHENIX (PHENIX.REFINE: 1.8.4_1496)                   
REMARK   3   AUTHORS     : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN            
REMARK   3               : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,           
REMARK   3               : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,            
REMARK   3               : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,              
REMARK   3               : REETAL PAI,RANDY READ,JANE RICHARDSON,               
REMARK   3               : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,           
REMARK   3               : NICHOLAS SAUTER,JACOB SMITH,LAURENT                  
REMARK   3               : STORONI,TOM TERWILLIGER,PETER ZWART                  
REMARK   3                                                                      
REMARK   3    REFINEMENT TARGET : ML                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 33.82                          
REMARK   3   MIN(FOBS/SIGMA_FOBS)              : 1.940                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 93.4                           
REMARK   3   NUMBER OF REFLECTIONS             : 2000                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   R VALUE     (WORKING + TEST SET) : 0.195                           
REMARK   3   R VALUE            (WORKING SET) : 0.193                           
REMARK   3   FREE R VALUE                     : 0.242                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 4.570                           
REMARK   3   FREE R VALUE TEST SET COUNT      : 159                             
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 33.8250 -  2.1810    0.93     3318   159  0.1925 0.2417        
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELLING.                                             
REMARK   3   METHOD USED        : FLAT BULK SOLVENT MODEL                       
REMARK   3   SOLVENT RADIUS     : 1.11                                          
REMARK   3   SHRINKAGE RADIUS   : 0.90                                          
REMARK   3   K_SOL              : NULL                                          
REMARK   3   B_SOL              : NULL                                          
REMARK   3                                                                      
REMARK   3  ERROR ESTIMATES.                                                    
REMARK   3   COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED)     : 0.220            
REMARK   3   PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 45.480           
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : NULL                           
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  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      :  0.005            289                                  
REMARK   3   ANGLE     :  1.915            454                                  
REMARK   3   CHIRALITY :  0.027             38                                  
REMARK   3   PLANARITY :  0.002             13                                  
REMARK   3   DIHEDRAL  : 28.048             97                                  
REMARK   3                                                                      
REMARK   3  TLS DETAILS                                                         
REMARK   3   NUMBER OF TLS GROUPS  : 1                                          
REMARK   3   TLS GROUP : 1                                                      
REMARK   3    SELECTION: CHAIN 'A'                                              
REMARK   3    ORIGIN FOR THE GROUP (A):  10.5399  11.9227 -19.6956              
REMARK   3    T TENSOR                                                          
REMARK   3      T11:   0.7892 T22:   0.7835                                     
REMARK   3      T33:   0.5859 T12:   0.0531                                     
REMARK   3      T13:  -0.0091 T23:  -0.0285                                     
REMARK   3    L TENSOR                                                          
REMARK   3      L11:   4.9133 L22:   6.1569                                     
REMARK   3      L33:   1.8969 L12:  -2.1317                                     
REMARK   3      L13:   2.0699 L23:  -2.6301                                     
REMARK   3    S TENSOR                                                          
REMARK   3      S11:  -0.0704 S12:   0.2214 S13:  -0.7320                       
REMARK   3      S21:  -0.3011 S22:   0.2186 S23:   0.1891                       
REMARK   3      S31:  -0.2632 S32:  -0.1487 S33:  -0.0333                       
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 4RE7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-14.                  
REMARK 100 THE DEPOSITION ID IS D_1000087235.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 10-JUL-14                          
REMARK 200  TEMPERATURE           (KELVIN) : 100                                
REMARK 200  PH                             : 7                                  
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : DIAMOND                            
REMARK 200  BEAMLINE                       : I02                                
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9795                             
REMARK 200  MONOCHROMATOR                  : DOUBLE CRYSTAL SI(111)             
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : PIXEL                              
REMARK 200  DETECTOR MANUFACTURER          : DECTRIS PILATUS 6M                 
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : XDS                                
REMARK 200  DATA SCALING SOFTWARE          : SCALA                              
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 2012                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 2.180                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 47.830                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 94.1                               
REMARK 200  DATA REDUNDANCY                : 10.50                              
REMARK 200  R MERGE                    (I) : 0.13700                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 11.5000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 2.24                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 93.0                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 10.70                              
REMARK 200  R MERGE FOR SHELL          (I) : 1.12200                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.900                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD                          
REMARK 200 SOFTWARE USED: SHELXCD                                               
REMARK 200 STARTING MODEL: NULL                                                 
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 59.40                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.03                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: 1 UL 2 MM OLIGONUCLEOTIDE (DOUBLE HPLC   
REMARK 280  -PURIFIED) + 1 UL 2 MM LAMBDA-[RU(TAP)2(DPPZ)]CL2 + 6 UL 10% V/V    
REMARK 280  MPD, 40 MM SODIUM CACODYLATE, PH 6.0, 12 MM SPERMINE                
REMARK 280  TETRAHYDROCHLORIDE, 80 MM SODIUM CHLORIDE, 20 MM BARIUM CHLORIDE    
REMARK 280  EQUILIBRATED AGAINST 1 ML 35% V/V MPD, VAPOR DIFFUSION, SITTING     
REMARK 280  DROP, TEMPERATURE 291K, PH 7                                        
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2                        
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,Z                                                   
REMARK 290       2555   -X,-Y,Z+1/2                                             
REMARK 290       3555   -Y+1/2,X+1/2,Z+3/4                                      
REMARK 290       4555   Y+1/2,-X+1/2,Z+1/4                                      
REMARK 290       5555   -X+1/2,Y+1/2,-Z+3/4                                     
REMARK 290       6555   X+1/2,-Y+1/2,-Z+1/4                                     
REMARK 290       7555   Y,X,-Z                                                  
REMARK 290       8555   -Y,-X,-Z+1/2                                            
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       16.05500            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000       23.91500            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000       23.91500            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       24.08250            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000       23.91500            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000       23.91500            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000        8.02750            
REMARK 290   SMTRY1   5 -1.000000  0.000000  0.000000       23.91500            
REMARK 290   SMTRY2   5  0.000000  1.000000  0.000000       23.91500            
REMARK 290   SMTRY3   5  0.000000  0.000000 -1.000000       24.08250            
REMARK 290   SMTRY1   6  1.000000  0.000000  0.000000       23.91500            
REMARK 290   SMTRY2   6  0.000000 -1.000000  0.000000       23.91500            
REMARK 290   SMTRY3   6  0.000000  0.000000 -1.000000        8.02750            
REMARK 290   SMTRY1   7  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   7  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   7  0.000000  0.000000 -1.000000        0.00000            
REMARK 290   SMTRY1   8  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   8 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   8  0.000000  0.000000 -1.000000       16.05500            
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: 1930 ANGSTROM**2                          
REMARK 350 SURFACE AREA OF THE COMPLEX: 4940 ANGSTROM**2                        
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL                        
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 350   BIOMT1   2  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT2   2  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT3   2  0.000000  0.000000 -1.000000      -32.11000            
REMARK 620                                                                      
REMARK 620 METAL COORDINATION                                                   
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;               
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):                             
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              BA A 101  BA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1  DI A   3   N7                                                     
REMARK 620 2  DG A   4   O6   75.2                                              
REMARK 620 N                    1                                               
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 101                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE RKL A 102                 
REMARK 900                                                                      
REMARK 900 RELATED ENTRIES                                                      
REMARK 900 RELATED ID: 3QRN   RELATED DB: PDB                                   
REMARK 900 LAMBDA-[RU(TAP)2(DPPZ)]2+ BOUND TO D(TCGGCGCCGA)                     
REMARK 900 RELATED ID: 4QIO   RELATED DB: PDB                                   
REMARK 900 LAMBDA-[RU(TAP)2(DPPZ)]2+ BOUND TO D(TCGGCGCCIA)                     
DBREF  4RE7 A    1    10  PDB    4RE7     4RE7             1     10             
SEQRES   1 A   10   DT  DC  DI  DG  DC  DG  DC  DC  DG  DA                      
HET     BA  A 101       1                                                       
HET    RKL  A 102      51                                                       
HETNAM      BA BARIUM ION                                                       
HETNAM     RKL RU(TAP)2(DPPZ) COMPLEX                                           
FORMUL   2   BA    BA 2+                                                        
FORMUL   3  RKL    C38 H22 N12 RU 2+                                            
FORMUL   4  HOH   *(H2 O)                                                       
LINK         N7   DI A   3                BA    BA A 101     1555   1555  2.91  
LINK         O6   DG A   4                BA    BA A 101     1555   1555  2.80  
SITE     1 AC1  2  DI A   3   DG A   4                                          
SITE     1 AC2  8  DT A   1   DC A   2   DI A   3   DG A   4                    
SITE     2 AC2  8  DC A   7   DC A   8   DG A   9   DA A  10                    
CRYST1   47.830   47.830   32.110  90.00  90.00  90.00 P 43 21 2     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      0.020907  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.020907  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.031143        0.00000