HEADER RNA 10-MAY-17 5VR4 TITLE RNA OCTAMER CONTAINING 2'-F-4'-OME U. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*GP*AP*AP*(UMO)P*UP*CP*G)-3'); COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.M.HARP,M.EGLI REVDAT 3 04-OCT-23 5VR4 1 REMARK REVDAT 2 25-OCT-17 5VR4 1 JRNL REVDAT 1 04-OCT-17 5VR4 0 JRNL AUTH E.MALEK-ADAMIAN,D.C.GUENTHER,S.MATSUDA,S.MARTINEZ-MONTERO, JRNL AUTH 2 I.ZLATEV,J.HARP,M.BURAI PATRASCU,D.J.FOSTER,J.FAKHOURY, JRNL AUTH 3 L.PERKINS,N.MOITESSIER,R.M.MANOHARAN,N.TANEJA,A.BISBE, JRNL AUTH 4 K.CHARISSE,M.MAIER,K.G.RAJEEV,M.EGLI,M.MANOHARAN,M.J.DAMHA JRNL TITL 4'-C-METHOXY-2'-DEOXY-2'-FLUORO MODIFIED RIBONUCLEOTIDES JRNL TITL 2 IMPROVE METABOLIC STABILITY AND ELICIT EFFICIENT JRNL TITL 3 RNAI-MEDIATED GENE SILENCING. JRNL REF J. AM. CHEM. SOC. V. 139 14542 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28937776 JRNL DOI 10.1021/JACS.7B07582 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.170 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 26152 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 1375 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 29.4867 - 3.2241 0.97 2434 121 0.1864 0.2256 REMARK 3 2 3.2241 - 2.5595 0.99 2473 151 0.1897 0.2415 REMARK 3 3 2.5595 - 2.2361 1.00 2495 124 0.1932 0.2679 REMARK 3 4 2.2361 - 2.0317 1.00 2482 148 0.1708 0.2692 REMARK 3 5 2.0317 - 1.8861 1.00 2503 159 0.1716 0.2204 REMARK 3 6 1.8861 - 1.7749 1.00 2444 156 0.1718 0.2039 REMARK 3 7 1.7749 - 1.6860 0.99 2518 108 0.1703 0.2631 REMARK 3 8 1.6860 - 1.6127 0.99 2495 133 0.1974 0.2514 REMARK 3 9 1.6127 - 1.5506 0.99 2481 142 0.2101 0.2598 REMARK 3 10 1.5506 - 1.4971 0.98 2452 133 0.2448 0.3200 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.40 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 : 0.009 754 REMARK 3 ANGLE : 1.804 1169 REMARK 3 CHIRALITY : 0.072 152 REMARK 3 PLANARITY : 0.037 36 REMARK 3 DIHEDRAL : 8.223 336 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5VR4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227191. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 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) : 0.97856 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26152 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.79500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.730 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3P4A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 MM RNA, 10 MM COBALT(III) REMARK 280 HEXAMINE, 6 MM SODIUM CHLORIDE, 40 MM POTASSIUM CHLORIDE, 5% MPD, REMARK 280 20 MM SODIUM CACODYLATE EQUILIBRATED AGAINST RESERVOIR REMARK 280 CONTAINING 40% MPD, PH 6.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 42.96050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 22.19350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 22.19350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.44075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 22.19350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 22.19350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.48025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 22.19350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 22.19350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 64.44075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 22.19350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 22.19350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 21.48025 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 42.96050 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 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 221 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 333 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 304 O HOH B 304 8554 1.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 CON C 201 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CON C 201 DBREF 5VR4 A 101 108 PDB 5VR4 5VR4 101 108 DBREF 5VR4 B 209 216 PDB 5VR4 5VR4 209 216 DBREF 5VR4 C 101 108 PDB 5VR4 5VR4 101 108 DBREF 5VR4 D 209 216 PDB 5VR4 5VR4 209 216 SEQRES 1 A 8 C G A A UMO U C G SEQRES 1 B 8 C G A A UMO U C G SEQRES 1 C 8 C G A A UMO U C G SEQRES 1 D 8 C G A A UMO U C G HET UMO A 105 33 HET UMO B 213 33 HET UMO C 105 33 HET UMO D 213 33 HET CON C 201 3 HETNAM UMO 2'-F-4'-OME U HETNAM CON COBALT TETRAAMMINE ION HETSYN UMO [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-BIS(OXIDANYLIDENE) HETSYN 2 UMO PYRIMIDIN-1-YL]-4-FLUORANYL-2-METHOXY-3-OXIDANYL- HETSYN 3 UMO OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE FORMUL 1 UMO 4(C10 H14 F N2 O9 P) FORMUL 5 CON CO H12 N4 3+ FORMUL 6 HOH *137(H2 O) LINK O3' A A 104 P UMO A 105 1555 1555 1.61 LINK O3' UMO A 105 P U A 106 1555 1555 1.62 LINK O3' A B 212 P UMO B 213 1555 1555 1.61 LINK O3' UMO B 213 P U B 214 1555 1555 1.61 LINK O3' A C 104 P UMO C 105 1555 1555 1.61 LINK O3' UMO C 105 P U C 106 1555 1555 1.62 LINK O3' A D 212 P UMO D 213 1555 1555 1.62 LINK O3' UMO D 213 P U D 214 1555 1555 1.61 SITE 1 AC1 1 A C 103 CRYST1 44.387 44.387 85.921 90.00 90.00 90.00 P 43 21 2 32 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 0.022529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011639 0.00000