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