HEADER    RNA                                     25-MAY-07   2Q1O              
TITLE     CRYSTAL STRUCTURE ANALYSIS OF THE RNA DODECAMER CGC-NF2-AAUUGGCG, WITH
TITLE    2 AN INCORPORATED 2,4-DIFLUOROTOLUYL RESIDUE (NF2)                     
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: RNA (5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*GP*GP*CP*G)-3');    
COMPND   3 CHAIN: A, B, C, D;                                                   
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED                                
KEYWDS    2, 4-DIFLUOROTOLUYL NUCLEOSIDE, CHEMICAL MODIFICATION, RNA, RNAI,     
KEYWDS   2 HYDROGEN BOND                                                        
EXPDTA    X-RAY DIFFRACTION                                                     
AUTHOR    F.LI,P.S.PALLAN                                                       
REVDAT   5   03-APR-24 2Q1O    1       REMARK                                   
REVDAT   4   21-FEB-24 2Q1O    1       DBREF  LINK                              
REVDAT   3   24-FEB-09 2Q1O    1       VERSN                                    
REVDAT   2   11-DEC-07 2Q1O    1       JRNL                                     
REVDAT   1   30-OCT-07 2Q1O    0                                                
JRNL        AUTH   F.LI,P.S.PALLAN,M.A.MAIER,K.G.RAJEEV,S.L.MATHIEU,C.KREUTZ,   
JRNL        AUTH 2 Y.FAN,J.SANGHVI,R.MICURA,E.ROZNERS,M.MANOHARAN,M.EGLI        
JRNL        TITL   CRYSTAL STRUCTURE, STABILITY AND IN VITRO RNAI ACTIVITY OF   
JRNL        TITL 2 OLIGORIBONUCLEOTIDES CONTAINING THE RIBO-DIFLUOROTOLUYL      
JRNL        TITL 3 NUCLEOTIDE: INSIGHTS INTO SUBSTRATE REQUIREMENTS BY THE      
JRNL        TITL 4 HUMAN RISC AGO2 ENZYME.                                      
JRNL        REF    NUCLEIC ACIDS RES.            V.  35  6424 2007              
JRNL        REFN                   ISSN 0305-1048                               
JRNL        PMID   17881374                                                     
JRNL        DOI    10.1093/NAR/GKM664                                           
REMARK   2                                                                      
REMARK   2 RESOLUTION.    1.10 ANGSTROMS.                                       
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : SHELXL-97                                            
REMARK   3   AUTHORS     : G.M.SHELDRICK                                        
REMARK   3                                                                      
REMARK   3  DATA USED IN REFINEMENT.                                            
REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10                           
REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : 10.00                          
REMARK   3   DATA CUTOFF            (SIGMA(F)) : 4.000                          
REMARK   3   COMPLETENESS FOR RANGE        (%) : 94.2                           
REMARK   3   CROSS-VALIDATION METHOD           : THROUGHOUT                     
REMARK   3   FREE R VALUE TEST SET SELECTION   : RANDOM                         
REMARK   3                                                                      
REMARK   3  FIT TO DATA USED IN REFINEMENT (NO CUTOFF).                         
REMARK   3   R VALUE   (WORKING + TEST SET, NO CUTOFF) : 0.114                  
REMARK   3   R VALUE          (WORKING SET, NO CUTOFF) : 0.110                  
REMARK   3   FREE R VALUE                  (NO CUTOFF) : 0.142                  
REMARK   3   FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (NO CUTOFF) : 2152                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (NO CUTOFF) : 45752                  
REMARK   3                                                                      
REMARK   3  FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).                     
REMARK   3   R VALUE   (WORKING + TEST SET, F>4SIG(F)) : NULL                   
REMARK   3   R VALUE          (WORKING SET, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE                  (F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL                   
REMARK   3   FREE R VALUE TEST SET COUNT   (F>4SIG(F)) : NULL                   
REMARK   3   TOTAL NUMBER OF REFLECTIONS   (F>4SIG(F)) : NULL                   
REMARK   3                                                                      
REMARK   3  NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.                    
REMARK   3   PROTEIN ATOMS      : 0                                             
REMARK   3   NUCLEIC ACID ATOMS : 1016                                          
REMARK   3   HETEROGEN ATOMS    : 0                                             
REMARK   3   SOLVENT ATOMS      : 323                                           
REMARK   3                                                                      
REMARK   3  MODEL REFINEMENT.                                                   
REMARK   3   OCCUPANCY SUM OF NON-HYDROGEN ATOMS      : NULL                    
REMARK   3   OCCUPANCY SUM OF HYDROGEN ATOMS          : NULL                    
REMARK   3   NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL                    
REMARK   3   NUMBER OF LEAST-SQUARES PARAMETERS       : NULL                    
REMARK   3   NUMBER OF RESTRAINTS                     : NULL                    
REMARK   3                                                                      
REMARK   3  RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.                        
REMARK   3   BOND LENGTHS                         (A) : NULL                    
REMARK   3   ANGLE DISTANCES                      (A) : 0.029                   
REMARK   3   SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL                    
REMARK   3   DISTANCES FROM RESTRAINT PLANES      (A) : NULL                    
REMARK   3   ZERO CHIRAL VOLUMES               (A**3) : NULL                    
REMARK   3   NON-ZERO CHIRAL VOLUMES           (A**3) : NULL                    
REMARK   3   ANTI-BUMPING DISTANCE RESTRAINTS     (A) : NULL                    
REMARK   3   RIGID-BOND ADP COMPONENTS         (A**2) : NULL                    
REMARK   3   SIMILAR ADP COMPONENTS            (A**2) : NULL                    
REMARK   3   APPROXIMATELY ISOTROPIC ADPS      (A**2) : NULL                    
REMARK   3                                                                      
REMARK   3  BULK SOLVENT MODELING.                                              
REMARK   3   METHOD USED: NULL                                                  
REMARK   3                                                                      
REMARK   3  STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER                        
REMARK   3   SPECIAL CASE: NULL                                                 
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: NULL                                      
REMARK   4                                                                      
REMARK   4 2Q1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-07.                  
REMARK 100 THE DEPOSITION ID IS D_1000043037.                                   
REMARK 200                                                                      
REMARK 200 EXPERIMENTAL DETAILS                                                 
REMARK 200  EXPERIMENT TYPE                : X-RAY DIFFRACTION                  
REMARK 200  DATE OF DATA COLLECTION        : 16-NOV-05                          
REMARK 200  TEMPERATURE           (KELVIN) : 120                                
REMARK 200  PH                             : 6                                  
REMARK 200  NUMBER OF CRYSTALS USED        : 1                                  
REMARK 200                                                                      
REMARK 200  SYNCHROTRON              (Y/N) : Y                                  
REMARK 200  RADIATION SOURCE               : APS                                
REMARK 200  BEAMLINE                       : 22-ID                              
REMARK 200  X-RAY GENERATOR MODEL          : NULL                               
REMARK 200  MONOCHROMATIC OR LAUE    (M/L) : M                                  
REMARK 200  WAVELENGTH OR RANGE        (A) : 0.9199                             
REMARK 200  MONOCHROMATOR                  : NULL                               
REMARK 200  OPTICS                         : NULL                               
REMARK 200                                                                      
REMARK 200  DETECTOR TYPE                  : CCD                                
REMARK 200  DETECTOR MANUFACTURER          : MARMOSAIC 300 MM CCD               
REMARK 200  INTENSITY-INTEGRATION SOFTWARE : HKL-2000                           
REMARK 200  DATA SCALING SOFTWARE          : HKL-2000                           
REMARK 200                                                                      
REMARK 200  NUMBER OF UNIQUE REFLECTIONS   : 45791                              
REMARK 200  RESOLUTION RANGE HIGH      (A) : 1.100                              
REMARK 200  RESOLUTION RANGE LOW       (A) : 42.450                             
REMARK 200  REJECTION CRITERIA  (SIGMA(I)) : 0.000                              
REMARK 200                                                                      
REMARK 200 OVERALL.                                                             
REMARK 200  COMPLETENESS FOR RANGE     (%) : 93.9                               
REMARK 200  DATA REDUNDANCY                : 3.400                              
REMARK 200  R MERGE                    (I) : 0.05900                            
REMARK 200  R SYM                      (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR THE DATA SET  : NULL                               
REMARK 200                                                                      
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.                                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10                     
REMARK 200  HIGHEST RESOLUTION SHELL, RANGE LOW  (A) : 1.14                     
REMARK 200  COMPLETENESS FOR SHELL     (%) : 90.7                               
REMARK 200  DATA REDUNDANCY IN SHELL       : 2.60                               
REMARK 200  R MERGE FOR SHELL          (I) : 0.23900                            
REMARK 200  R SYM FOR SHELL            (I) : NULL                               
REMARK 200  <I/SIGMA(I)> FOR SHELL         : NULL                               
REMARK 200                                                                      
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH                              
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT        
REMARK 200 SOFTWARE USED: EPMR                                                  
REMARK 200 STARTING MODEL: MODEL OF NATIVE A-RNA                                
REMARK 200                                                                      
REMARK 200 REMARK: NULL                                                         
REMARK 280                                                                      
REMARK 280 CRYSTAL                                                              
REMARK 280 SOLVENT CONTENT, VS   (%): 39.18                                     
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02                     
REMARK 280                                                                      
REMARK 280 CRYSTALLIZATION CONDITIONS: DROPLETS CONTAINING 0.5 MM               
REMARK 280  OLIGONUCLEOTIDE, 0.8 M AMMONIUM SULFATE, 0.05 M MES, PH 6.0,        
REMARK 280  WERE EQUILIBRATED AGAINST A RESERVOIR OF 1.6 M AMMONIUM SULFATE,    
REMARK 280  0.1 M MES, PH 6.0. , VAPOR DIFFUSION, SITTING DROP, TEMPERATURE     
REMARK 280  291K                                                                
REMARK 290                                                                      
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY                                            
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1                              
REMARK 290                                                                      
REMARK 290      SYMOP   SYMMETRY                                                
REMARK 290     NNNMMM   OPERATOR                                                
REMARK 290       1555   X,Y,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                                                                      
REMARK 290 REMARK: NULL                                                         
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1, 2                                                    
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: 1210 ANGSTROM**2                          
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 350                                                                      
REMARK 350 BIOMOLECULE: 2                                                       
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: 1190 ANGSTROM**2                          
REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D                                  
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 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
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   RES CSSEQI ATM2   DEVIATION                     
REMARK 500      G B 110   N7      G B 110   C8      0.040                       
REMARK 500      G C 102   C2'     G C 102   C1'    -0.051                       
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
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      A A 105   N9  -  C4  -  C5  ANGL. DEV. =   2.6 DEGREES          
REMARK 500      G B 109   C6  -  N1  -  C2  ANGL. DEV. =   4.0 DEGREES          
REMARK 500      G B 109   N1  -  C2  -  N3  ANGL. DEV. =  -3.6 DEGREES          
REMARK 500      G B 109   N7  -  C8  -  N9  ANGL. DEV. =   4.3 DEGREES          
REMARK 500      U C 107   C4  -  C5  -  C6  ANGL. DEV. =  -4.3 DEGREES          
REMARK 500      U C 107   C5  -  C6  -  N1  ANGL. DEV. =   4.5 DEGREES          
REMARK 500      U C 107   C5  -  C4  -  O4  ANGL. DEV. =  -4.7 DEGREES          
REMARK 500      G D 102   C3' -  C2' -  C1' ANGL. DEV. =  -5.1 DEGREES          
REMARK 500      G D 109   N1  -  C6  -  O6  ANGL. DEV. =   6.2 DEGREES          
REMARK 500      G D 109   C5  -  C6  -  O6  ANGL. DEV. =  -4.0 DEGREES          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  2Q1O A  101   112  PDB    2Q1O     2Q1O           101    112             
DBREF  2Q1O B  101   112  PDB    2Q1O     2Q1O           101    112             
DBREF  2Q1O C  101   112  PDB    2Q1O     2Q1O           101    112             
DBREF  2Q1O D  101   112  PDB    2Q1O     2Q1O           101    112             
SEQRES   1 A   12    C   G   C NF2   A   A   U   U   G   G   C   G              
SEQRES   1 B   12    C   G   C NF2   A   A   U   U   G   G   C   G              
SEQRES   1 C   12    C   G   C NF2   A   A   U   U   G   G   C   G              
SEQRES   1 D   12    C   G   C NF2   A   A   U   U   G   G   C   G              
HET    NF2  A 104      21                                                       
HET    NF2  B 104      21                                                       
HET    NF2  C 104      21                                                       
HET    NF2  D 104      21                                                       
HETNAM     NF2 (1S)-1,4-ANHYDRO-1-(2,4-DIFLUORO-5-METHYLPHENYL)-5-O-            
HETNAM   2 NF2  PHOSPHONO-D-RIBITOL                                             
FORMUL   1  NF2    4(C12 H15 F2 O7 P)                                           
FORMUL   5  HOH   *323(H2 O)                                                    
LINK         O3'   C A 103                 P   NF2 A 104     1555   1555  1.62  
LINK         O3' NF2 A 104                 P     A A 105     1555   1555  1.59  
LINK         O3'   C B 103                 P   NF2 B 104     1555   1555  1.59  
LINK         O3' NF2 B 104                 P     A B 105     1555   1555  1.60  
LINK         O3'   C C 103                 P   NF2 C 104     1555   1555  1.59  
LINK         O3' NF2 C 104                 P     A C 105     1555   1555  1.61  
LINK         O3'   C D 103                 P   NF2 D 104     1555   1555  1.58  
LINK         O3' NF2 D 104                 P     A D 105     1555   1555  1.60  
CRYST1   22.900   32.060   42.930  96.24  83.87  93.91 P 1           4          
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      0.043668  0.002985 -0.004408        0.00000                         
SCALE2      0.000000  0.031264  0.003213        0.00000                         
SCALE3      0.000000  0.000000  0.023551        0.00000