HEADER RNA 04-MAR-06 2G92 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE RNA DODECAMER CGC-(NF2)-AAUUAGCG, TITLE 2 WITH AN INCORPORATED 2,4-DIFLUOROTOLUYL RESIDUE (NF2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*GP*CP*(NF2)P*AP*AP*UP*UP*AP*GP*CP*G)-3'; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES KEYWDS 2, 4-DIFLUOROTOLUYL NUCLEOSIDE, CHEMICAL MODIFICATION, RNA, RNA KEYWDS 2 INTERFERENCE, HYDROGEN BONDING EXPDTA X-RAY DIFFRACTION AUTHOR M.EGLI,F.LI REVDAT 6 03-APR-24 2G92 1 REMARK REVDAT 5 14-FEB-24 2G92 1 REMARK LINK REVDAT 4 18-OCT-17 2G92 1 REMARK REVDAT 3 24-FEB-09 2G92 1 VERSN REVDAT 2 08-JUL-08 2G92 1 JRNL REVDAT 1 18-APR-06 2G92 0 JRNL AUTH J.XIA,A.NORONHA,I.TOUDJARSKA,F.LI,A.AKINC,R.BRAICH, JRNL AUTH 2 M.FRANK-KAMENETSKY,K.G.RAJEEV,M.EGLI,M.MANOHARAN JRNL TITL GENE SILENCING ACTIVITY OF SIRNAS WITH A RIBO-DIFLUOROTOLUYL JRNL TITL 2 NUCLEOTIDE. JRNL REF ACS CHEM.BIOL. V. 1 176 2006 JRNL REFN ISSN 1554-8929 JRNL PMID 17163665 JRNL DOI 10.1021/CB600063P REMARK 2 REMARK 2 RESOLUTION. 1.61 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 7425 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 + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.500 REMARK 3 FREE R VALUE TEST SET COUNT : 558 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 497 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 42 REMARK 3 BIN FREE R VALUE : 0.2650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 506 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 84 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -1.55000 REMARK 3 B12 (A**2) : 0.52000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.206 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.113 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.088 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.698 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 564 ; 0.012 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 200 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 860 ; 2.066 ; 3.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): 524 ; 1.504 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 116 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 246 ; 0.019 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 89 ; 0.182 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 279 ; 0.281 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 224 ; 0.251 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 130 ; 0.131 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 53 ; 0.356 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.422 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 14 ; 0.086 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 19 ; 0.177 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.311 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 798 ; 4.323 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 860 ; 5.042 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 12 REMARK 3 RESIDUE RANGE : B 13 B 24 REMARK 3 ORIGIN FOR THE GROUP (A): 4.4067 12.3175 14.3016 REMARK 3 T TENSOR REMARK 3 T11: 0.0125 T22: 0.0292 REMARK 3 T33: 0.0001 T12: 0.0032 REMARK 3 T13: -0.0050 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 0.0146 L22: 0.3351 REMARK 3 L33: 0.2382 L12: -0.0044 REMARK 3 L13: 0.0585 L23: 0.0179 REMARK 3 S TENSOR REMARK 3 S11: -0.0252 S12: 0.0302 S13: 0.0025 REMARK 3 S21: 0.0317 S22: -0.0130 S23: 0.0001 REMARK 3 S31: -0.0414 S32: 0.0376 S33: 0.0382 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2G92 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036841. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 5ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.992 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7538 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 24.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 1.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05400 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) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 1.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53000 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 (%): 36.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: FINAL DROPLET COMPOSITION: 0.5 MM REMARK 280 OLIGONUCLEOTIDE, 5% MPD, 20 MM SODIUM CACODYLATE, PH 5.5, 10 MM REMARK 280 COBALT HEXAMINE, 20 MM LICL AND 10 MM MGCL2., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.05700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.11400 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 DUPLEX AND CORRESPONDS TO THE REMARK 300 CRYSTALLOGRAPHIC ASYMMETRIC UNIT, HENCE NO SYMMETRY OPERATORS ARE REMARK 300 NEEDED 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 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 G A 2 C5 - C6 - O6 ANGL. DEV. = -4.4 DEGREES REMARK 500 U A 7 O5' - C5' - C4' ANGL. DEV. = -5.2 DEGREES REMARK 500 U A 8 N1 - C2 - O2 ANGL. DEV. = 4.3 DEGREES REMARK 500 G A 10 O4' - C1' - N9 ANGL. DEV. = 4.5 DEGREES REMARK 500 A B 17 O3' - P - OP1 ANGL. DEV. = 7.6 DEGREES REMARK 500 A B 17 N9 - C4 - C5 ANGL. DEV. = 2.8 DEGREES REMARK 500 A B 17 N1 - C6 - N6 ANGL. DEV. = -3.9 DEGREES REMARK 500 U B 19 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 U B 19 C4' - C3' - C2' ANGL. DEV. = -6.7 DEGREES REMARK 500 G B 24 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NF2 A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NF2 B 16 DBREF 2G92 A 1 12 PDB 2G92 2G92 1 12 DBREF 2G92 B 13 24 PDB 2G92 2G92 13 24 SEQRES 1 A 12 C G C NF2 A A U U A G C G SEQRES 1 B 12 C G C NF2 A A U U A G C G HET NF2 A 4 21 HET NF2 B 16 21 HETNAM NF2 (1S)-1,4-ANHYDRO-1-(2,4-DIFLUORO-5-METHYLPHENYL)-5-O- HETNAM 2 NF2 PHOSPHONO-D-RIBITOL FORMUL 1 NF2 2(C12 H15 F2 O7 P) FORMUL 3 HOH *84(H2 O) LINK O3' C A 3 P NF2 A 4 1555 1555 1.58 LINK O3' NF2 A 4 P A A 5 1555 1555 1.60 LINK O3' C B 15 P NF2 B 16 1555 1555 1.57 LINK O3' NF2 B 16 P A B 17 1555 1555 1.59 SITE 1 AC1 2 HOH A 105 HOH A 158 SITE 1 AC2 2 HOH B 138 HOH B 163 CRYST1 28.614 28.614 63.171 90.00 90.00 120.00 P 31 6 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 0.034948 0.020177 0.000000 0.00000 SCALE2 0.000000 0.040354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015830 0.00000