HEADER RNA 04-APR-18 6CXZ TITLE RNA OCTAMER CONTAINING 2'-F, 4'-CALPHA-ME U. COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*CP*GP*AP*AP*(U4M)P*UP*CP*G)-3'); COMPND 3 CHAIN: A, B; 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, OLIGONUCLEOTIDE, MODIFIED BASE EXPDTA X-RAY DIFFRACTION AUTHOR J.M.HARP,M.EGLI REVDAT 3 04-OCT-23 6CXZ 1 REMARK REVDAT 2 03-OCT-18 6CXZ 1 JRNL REVDAT 1 29-AUG-18 6CXZ 0 JRNL AUTH J.M.HARP,D.C.GUENTHER,A.BISBE,L.PERKINS,S.MATSUDA, JRNL AUTH 2 G.R.BOMMINENI,I.ZLATEV,D.J.FOSTER,N.TANEJA,K.CHARISSE, JRNL AUTH 3 M.A.MAIER,K.G.RAJEEV,M.MANOHARAN,M.EGLI JRNL TITL STRUCTURAL BASIS FOR THE SYNERGY OF 4'- AND 2'-MODIFICATIONS JRNL TITL 2 ON SIRNA NUCLEASE RESISTANCE, THERMAL STABILITY AND RNAI JRNL TITL 3 ACTIVITY. JRNL REF NUCLEIC ACIDS RES. V. 46 8090 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30107495 JRNL DOI 10.1093/NAR/GKY703 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2992 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) : 24.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.270 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 6672 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.420 REMARK 3 FREE R VALUE TEST SET COUNT : 519 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 24.4422 - 2.3799 0.99 2780 141 0.1722 0.2070 REMARK 3 2 2.3799 - 1.8892 1.00 2803 130 0.1966 0.2181 REMARK 3 3 1.8892 - 1.6505 1.00 2846 125 0.1852 0.1925 REMARK 3 4 1.6505 - 1.4996 0.99 2801 123 0.2426 0.3034 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.670 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.21 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6CXZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233658. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6684 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 21.60 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.98800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: PHENIX REMARK 200 STARTING MODEL: 5VR4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 MM RNA, 40 MM NA CACODYLATE, 20 MM REMARK 280 MAGNESIUM CHLORIDE, 20 MM COBALT(3+) HEXAMINE CHLORIDE, 40% MPD, REMARK 280 PH 6.5, VAPOR DIFFUSION, SITTING DROP, 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 40.94450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 15.23000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 15.23000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.41675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 15.23000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 15.23000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.47225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 15.23000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 15.23000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 61.41675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 15.23000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 15.23000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 20.47225 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 40.94450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 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 225 LIES ON A SPECIAL POSITION. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CAC A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NCO B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide A B 4 and U4M B 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VR4 RELATED DB: PDB REMARK 900 5VR4 CONTAINS A 4'-MODIFIED RNA DBREF 6CXZ A 1 8 PDB 6CXZ 6CXZ 1 8 DBREF 6CXZ B 1 8 PDB 6CXZ 6CXZ 1 8 SEQRES 1 A 8 C G A A U4M U C G SEQRES 1 B 8 C G A A U4M U C G HET U4M A 5 33 HET U4M B 5 33 HET CAC A 101 5 HET NCO B 101 7 HETNAM U4M 1-{2,5-DIDEOXY-2-FLUORO-4-[(PHOSPHONOOXY)METHYL]-ALPHA- HETNAM 2 U4M L-LYXOFURANOSYL}PYRIMIDINE-2,4(1H,3H)-DIONE HETNAM CAC CACODYLATE ION HETNAM NCO COBALT HEXAMMINE(III) HETSYN U4M 2'-F,4'-ALPHA-METHYL URIDINE 5--(DIHYDROGEN PHOSPHATE) HETSYN CAC DIMETHYLARSINATE FORMUL 1 U4M 2(C10 H14 F N2 O8 P) FORMUL 3 CAC C2 H6 AS O2 1- FORMUL 4 NCO CO H18 N6 3+ FORMUL 5 HOH *51(H2 O) LINK O3' A A 4 P U4M A 5 1555 1555 1.61 LINK O3' U4M A 5 P U A 6 1555 1555 1.60 LINK O3' A B 4 P U4M B 5 1555 1555 1.61 LINK O3' U4M B 5 P U B 6 1555 1555 1.61 SITE 1 AC1 4 U A 6 C A 7 A B 4 U4M B 5 SITE 1 AC2 6 A A 4 C B 1 G B 2 C B 7 SITE 2 AC2 6 G B 8 HOH B 204 SITE 1 AC3 15 C A 1 A A 4 U4M A 5 U A 6 SITE 2 AC3 15 G A 8 CAC A 101 HOH A 203 A B 3 SITE 3 AC3 15 U B 6 HOH B 202 HOH B 208 HOH B 210 SITE 4 AC3 15 HOH B 214 HOH B 218 HOH B 221 CRYST1 30.460 30.460 81.889 90.00 90.00 90.00 P 43 21 2 16 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 0.032830 0.000000 0.000000 0.00000 SCALE2 0.000000 0.032830 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012212 0.00000