HEADER    RNA                                     12-NOV-01   1KD4              
TITLE     THE CRYSTAL STRUCTURE OF R(GGUCACAGCCC)2, BARIUM FORM                 
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-R(*GP*GP*UP*CP*AP*CP*AP*GP*CP*CP*C)-3';                 
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES                                                       
KEYWDS    RNA DUPLEX, METAL BINDING, RNA                                        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    V.KACER,S.A.SCARINGE,J.N.SCARSDALE,J.P.RIFE                           
REVDAT   3   07-FEB-24 1KD4    1       REMARK LINK                              
REVDAT   2   24-FEB-09 1KD4    1       VERSN                                    
REVDAT   1   04-MAR-03 1KD4    0                                                
JRNL        AUTH   V.KACER,S.A.SCARINGE,J.N.SCARSDALE,J.P.RIFE                  
JRNL        TITL   CRYSTAL STRUCTURES OF R(GGUCACAGCCC)2.                       
JRNL        REF    ACTA CRYSTALLOGR.,SECT.D      V.  59   423 2003              
JRNL        REFN                   ISSN 0907-4449                               
JRNL        PMID   12595698                                                     
JRNL        DOI    10.1107/S0907444902021911                                    
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.85 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : CNS                                                  
REMARK   3   AUTHORS     : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-              
REMARK   3               : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,              
REMARK   3               : READ,RICE,SIMONSON,WARREN                            
REMARK   3                                                                      
REMARK   3  REFINEMENT TARGET : NULL                                            
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 20.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 2.000                          
REMARK   3   DATA CUTOFF HIGH         (ABS(F)) : 583553.360                     
REMARK   3   DATA CUTOFF LOW          (ABS(F)) : 0.0000                         
REMARK   3   COMPLETENESS (WORKING+TEST)   (%) : 97.9                           
REMARK   3   NUMBER OF REFLECTIONS             : 6991                           
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT.                                     
REMARK   3   CROSS-VALIDATION METHOD          : THROUGHOUT                      
REMARK   3   FREE R VALUE TEST SET SELECTION  : RANDOM                          
REMARK   3   R VALUE            (WORKING SET) : 0.203                           
REMARK   3   FREE R VALUE                     : 0.222                           
REMARK   3   FREE R VALUE TEST SET SIZE   (%) : 10.800                          
REMARK   3   FREE R VALUE TEST SET COUNT      : 756                             
REMARK   3   ESTIMATED ERROR OF FREE R VALUE  : 0.008                           
REMARK   3                                                                      
REMARK   3  FIT IN THE HIGHEST RESOLUTION BIN.                                  
REMARK   3   TOTAL NUMBER OF BINS USED           : 6                            
REMARK   3   BIN RESOLUTION RANGE HIGH       (A) : 1.85                         
REMARK   3   BIN RESOLUTION RANGE LOW        (A) : 1.97                         
REMARK   3   BIN COMPLETENESS (WORKING+TEST) (%) : 95.10                        
REMARK   3   REFLECTIONS IN BIN    (WORKING SET) : 1000                         
REMARK   3   BIN R VALUE           (WORKING SET) : 0.2440                       
REMARK   3   BIN FREE R VALUE                    : 0.2770                       
REMARK   3   BIN FREE R VALUE TEST SET SIZE  (%) : 11.00                        
REMARK   3   BIN FREE R VALUE TEST SET COUNT     : 123                          
REMARK   3   ESTIMATED ERROR OF BIN FREE R VALUE : 0.025                        
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS            : 0                                       
REMARK   3   NUCLEIC ACID ATOMS       : 460                                     
REMARK   3   HETEROGEN ATOMS          : 2                                       
REMARK   3   SOLVENT ATOMS            : 69                                      
REMARK   3                                                                      
REMARK   3  B VALUES.                                                           
REMARK   3   FROM WILSON PLOT           (A**2) : 25.80                          
REMARK   3   MEAN B VALUE      (OVERALL, A**2) : 29.00                          
REMARK   3   OVERALL ANISOTROPIC B VALUE.                                       
REMARK   3    B11 (A**2) : -0.03000                                             
REMARK   3    B22 (A**2) : -0.03000                                             
REMARK   3    B33 (A**2) : 0.05000                                              
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 COORDINATE ERROR.                                         
REMARK   3   ESD FROM LUZZATI PLOT        (A) : 0.21                            
REMARK   3   ESD FROM SIGMAA              (A) : 0.17                            
REMARK   3   LOW RESOLUTION CUTOFF        (A) : 5.00                            
REMARK   3                                                                      
REMARK   3  CROSS-VALIDATED ESTIMATED COORDINATE ERROR.                         
REMARK   3   ESD FROM C-V LUZZATI PLOT    (A) : 0.23                            
REMARK   3   ESD FROM C-V SIGMAA          (A) : 0.20                            
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM IDEAL VALUES.                                   
REMARK   3   BOND LENGTHS                 (A) : 0.004                           
REMARK   3   BOND ANGLES            (DEGREES) : 0.900                           
REMARK   3   DIHEDRAL ANGLES        (DEGREES) : 10.30                           
REMARK   3   IMPROPER ANGLES        (DEGREES) : 1.340                           
REMARK   3                                                                      
REMARK   3  ISOTROPIC THERMAL MODEL : RESTRAINED                                
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  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED : FLAT MODEL                                           
REMARK   3   KSOL        : 0.42                                                 
REMARK   3   BSOL        : 51.12                                                
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  : DNA-RNA_REP.PARAM                              
REMARK   3  PARAMETER FILE  2  : WATER_REP.PARAM                                
REMARK   3  PARAMETER FILE  3  : BAR.PARAM                                      
REMARK   3  PARAMETER FILE  4  : NULL                                           
REMARK   3  TOPOLOGY FILE  1   : DNA-RNA.TOP                                    
REMARK   3  TOPOLOGY FILE  2   : WATER.TOP                                      
REMARK   3  TOPOLOGY FILE  3   : BAR.TOP                                        
REMARK   3  TOPOLOGY FILE  4   : NULL                                           
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 1KD4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-01.                  
REMARK 100 THE DEPOSITION ID IS D_1000014829.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 05-JUN-00                          
REMARK 200  TEMPERATURE           (KELVIN) : 98                                 
REMARK 200  PH                             : 6.0                                
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                  : OSMIC CONFOCAL OPTICS              
REMARK 200  OPTICS                         : OSMIC CONFOCAL OPTICS              
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : IMAGE PLATE                        
REMARK 200  DETECTOR MANUFACTURER          : RIGAKU RAXIS IIC                   
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : DENZO, TRUNCATE                    
REMARK 200  DATA SCALING SOFTWARE          : SCALEPACK, CCP4 (TRUNCATE)         
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 7128                               
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.850                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 20.000                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : -3.000                             
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 99.7                               
REMARK 200  DATA REDUNDANCY                : 4.600                              
REMARK 200  R MERGE                    (I) : 0.09200                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : 19.9000                            
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.88                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 98.4                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 4.60                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.40000                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : 1.800                              
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: CNS                                                   
REMARK 200 STARTING MODEL: METAL FREE R(GGUCACAGCCC)2                           
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 56.20                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: MPD, 40MM NA CACODYLATE (PH 6.0), 12     
REMARK 280  MM SPERMINE 4HCL, 80 MM KCL, 20 MM BACL2, VAPOR DIFFUSION,          
REMARK 280  HANGING DROP AT 293K                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43                             
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,X,Z+3/4                                              
REMARK 290       4555   Y,-X,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        0.00000            
REMARK 290   SMTRY2   2  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY3   2  0.000000  0.000000  1.000000       26.31000            
REMARK 290   SMTRY1   3  0.000000 -1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   3  1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   3  0.000000  0.000000  1.000000       39.46500            
REMARK 290   SMTRY1   4  0.000000  1.000000  0.000000        0.00000            
REMARK 290   SMTRY2   4 -1.000000  0.000000  0.000000        0.00000            
REMARK 290   SMTRY3   4  0.000000  0.000000  1.000000       13.15500            
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 APPLY THE FOLLOWING TO CHAINS: A, B                                  
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 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 502  BA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1   G A   2   O6                                                     
REMARK 620 2   U A   3   O4   73.9                                              
REMARK 620 3 HOH A  70   O    71.0  69.4                                        
REMARK 620 4 HOH A 147   O    64.9 129.2  70.0                                  
REMARK 620 5   G B   8   O6   66.6  76.2 131.0 110.7                            
REMARK 620 6 HOH B  72   O   135.4  84.2 135.9 146.5  70.6                      
REMARK 620 7 HOH B  75   O   106.1 153.3 136.7  70.1  79.5  77.6                
REMARK 620 8 HOH B  82   O   135.5  68.2  74.4 126.3 123.0  63.0 118.3          
REMARK 620 9 HOH B 141   O   130.2 133.2  81.5  67.0 146.1  93.1  67.8  69.1    
REMARK 620 N                    1     2     3     4     5     6     7     8     
REMARK 620                                                                      
REMARK 620 COORDINATION ANGLES FOR:  M RES CSSEQI METAL                         
REMARK 620                              BA B 501  BA                            
REMARK 620 N RES CSSEQI ATOM                                                    
REMARK 620 1   G A   8   O6                                                     
REMARK 620 2 HOH A  73   O    76.3                                              
REMARK 620 3 HOH A  81   O    67.6  73.9                                        
REMARK 620 4 HOH A 174   O   123.7 121.3  68.2                                  
REMARK 620 5 HOH A 175   O   148.5  73.1  96.6  68.8                            
REMARK 620 6   G B   2   O6   65.5 105.4 131.6 133.3 130.2                      
REMARK 620 7   U B   3   O4   77.0 151.0  85.7  66.7 130.8  72.9                
REMARK 620 8 HOH B  84   O   109.7  73.2 146.5 126.4  68.0  64.4 127.1          
REMARK 620 9 HOH B 134   O   131.2 140.8 137.3  70.9  79.1  72.6  67.4  71.1    
REMARK 620 N                    1     2     3     4     5     6     7     8     
REMARK 800                                                                      
REMARK 800 SITE                                                                 
REMARK 800 SITE_IDENTIFIER: AC1                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA B 501                  
REMARK 800                                                                      
REMARK 800 SITE_IDENTIFIER: AC2                                                 
REMARK 800 EVIDENCE_CODE: SOFTWARE                                              
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BA A 502                  
DBREF  1KD4 A    1    11  PDB    1KD4     1KD4             1     11             
DBREF  1KD4 B    1    11  PDB    1KD4     1KD4             1     11             
SEQRES   1 A   11    G   G   U   C   A   C   A   G   C   C   C                  
SEQRES   1 B   11    G   G   U   C   A   C   A   G   C   C   C                  
HET     BA  A 502       1                                                       
HET     BA  B 501       1                                                       
HETNAM      BA BARIUM ION                                                       
FORMUL   3   BA    2(BA 2+)                                                     
FORMUL   5  HOH   *69(H2 O)                                                     
LINK         O6    G A   2                BA    BA A 502     1555   1555  2.81  
LINK         O4    U A   3                BA    BA A 502     1555   1555  2.73  
LINK         O6    G A   8                BA    BA B 501     1555   1555  2.93  
LINK         O   HOH A  70                BA    BA A 502     1555   1555  2.73  
LINK         O   HOH A  73                BA    BA B 501     1555   1555  2.67  
LINK         O   HOH A  81                BA    BA B 501     1555   1555  2.81  
LINK         O   HOH A 147                BA    BA A 502     1555   1555  2.76  
LINK         O   HOH A 174                BA    BA B 501     1555   1555  2.80  
LINK         O   HOH A 175                BA    BA B 501     1555   1555  2.68  
LINK        BA    BA A 502                 O6    G B   8     1555   1555  2.94  
LINK        BA    BA A 502                 O   HOH B  72     1555   1555  2.75  
LINK        BA    BA A 502                 O   HOH B  75     1555   1555  2.71  
LINK        BA    BA A 502                 O   HOH B  82     1555   1555  2.82  
LINK        BA    BA A 502                 O   HOH B 141     1555   1555  2.74  
LINK         O6    G B   2                BA    BA B 501     1555   1555  2.81  
LINK         O4    U B   3                BA    BA B 501     1555   1555  2.70  
LINK         O   HOH B  84                BA    BA B 501     1555   1555  2.66  
LINK         O   HOH B 134                BA    BA B 501     1555   1555  2.71  
SITE     1 AC1  9   G A   8  HOH A  73  HOH A  81  HOH A 174                    
SITE     2 AC1  9 HOH A 175    G B   2    U B   3  HOH B  84                    
SITE     3 AC1  9 HOH B 134                                                     
SITE     1 AC2  9   G A   2    U A   3  HOH A  70  HOH A 147                    
SITE     2 AC2  9   G B   8  HOH B  72  HOH B  75  HOH B  82                    
SITE     3 AC2  9 HOH B 141                                                     
CRYST1   39.990   39.990   52.620  90.00  90.00  90.00 P 43          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      0.025006  0.000000  0.000000        0.00000                         
SCALE2      0.000000  0.025006  0.000000        0.00000                         
SCALE3      0.000000  0.000000  0.019004        0.00000