HEADER RNA 22-JUL-14 4U3L TITLE OCTAMERIC RNA DUPLEX CO-CRYSTALLIZED IN CALCIUM(II)CHLORIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*UP*CP*GP*UP*AP*CP*GP*A)-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, DUPLEX, DI- AND TRIVALENT METAL IONS EXPDTA X-RAY DIFFRACTION AUTHOR M.F.SCHAFFER,B.SPINGLER,J.SCHNABL,G.PENG,V.OLIERIC,R.K.O.SIGEL REVDAT 2 13-JUL-16 4U3L 1 JRNL REVDAT 1 29-JUL-15 4U3L 0 JRNL AUTH M.F.SCHAFFER,G.PENG,B.SPINGLER,J.SCHNABL,M.WANG,V.OLIERIC, JRNL AUTH 2 R.K.SIGEL JRNL TITL THE X-RAY STRUCTURES OF SIX OCTAMERIC RNA DUPLEXES IN THE JRNL TITL 2 PRESENCE OF DIFFERENT DI- AND TRIVALENT CATIONS. JRNL REF INT J MOL SCI V. 17 2016 JRNL REFN ESSN 1422-0067 JRNL PMID 27355942 JRNL DOI 10.3390/IJMS17070988 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.320 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 14193 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 708 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 32.3131 - 2.5332 0.97 2699 138 0.1498 0.1707 REMARK 3 2 2.5332 - 2.0107 0.98 2679 143 0.1935 0.2063 REMARK 3 3 2.0107 - 1.7566 0.98 2762 146 0.1839 0.1714 REMARK 3 4 1.7566 - 1.5960 0.98 2709 142 0.1803 0.2288 REMARK 3 5 1.5960 - 1.4816 0.96 2636 139 0.2322 0.2771 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.005 372 REMARK 3 ANGLE : 0.956 576 REMARK 3 CHIRALITY : 0.040 78 REMARK 3 PLANARITY : 0.010 16 REMARK 3 DIHEDRAL : 8.562 184 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 4U3L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000202752. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.61 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14194 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.482 REMARK 200 RESOLUTION RANGE LOW (A) : 32.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG 400, 0.2 M CALCIUM CHLORIDE, REMARK 280 0.002 M SPERMINE, 0.05 HEPES SODIUM BUFFER PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.83550 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 13.76143 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.29500 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 23.83550 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 13.76143 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 17.29500 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 23.83550 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 13.76143 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 17.29500 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.52286 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 34.59000 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.52286 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 34.59000 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.52286 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 34.59000 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: 1150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 2990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 CA CA A 102 LIES ON A SPECIAL POSITION. REMARK 375 CA CA B 101 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 209 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 208 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 210 O HOH B 214 2.11 REMARK 500 OP1 A A 5 O HOH A 201 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 4 O4 REMARK 620 2 HOH A 215 O 75.8 REMARK 620 3 HOH B 216 O 143.7 74.0 REMARK 620 4 HOH A 212 O 87.5 109.7 84.1 REMARK 620 5 HOH A 214 O 71.8 146.1 139.8 78.7 REMARK 620 6 HOH B 219 O 143.3 133.7 73.0 98.2 73.9 REMARK 620 7 HOH B 220 O 91.8 80.9 102.8 168.8 90.5 75.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 7 OP1 REMARK 620 2 HOH A 208 O 81.9 REMARK 620 3 G A 7 OP1 0.0 81.9 REMARK 620 4 HOH A 208 O 171.4 89.7 171.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 5 O2' REMARK 620 2 HOH B 208 O 122.8 REMARK 620 3 A B 5 O2' 0.0 122.8 REMARK 620 4 HOH B 208 O 122.9 0.1 122.9 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 101 DBREF 4U3L A 1 8 PDB 4U3L 4U3L 1 8 DBREF 4U3L B 1 8 PDB 4U3L 4U3L 1 8 SEQRES 1 A 8 U C G U A C G A SEQRES 1 B 8 U C G U A C G A HET CA A 101 1 HET CA A 102 1 HET CA B 101 1 HETNAM CA CALCIUM ION FORMUL 3 CA 3(CA 2+) FORMUL 6 HOH *53(H2 O) LINK O4 U A 4 CA CA A 101 1555 1555 2.39 LINK OP1 G A 7 CA CA A 102 1555 1555 2.34 LINK O2' A B 5 CA CA B 101 1555 1555 2.86 LINK CA CA A 101 O HOH A 215 1555 1555 2.40 LINK CA CA A 101 O HOH B 216 1555 1555 2.46 LINK CA CA A 101 O HOH A 212 1555 1555 2.43 LINK CA CA A 101 O HOH A 214 1555 1555 2.40 LINK CA CA A 101 O HOH B 219 1555 1555 2.37 LINK CA CA A 101 O HOH B 220 1555 1555 2.35 LINK CA CA A 102 O HOH A 208 1555 1555 2.51 LINK CA CA B 101 O HOH B 208 1555 1555 3.16 LINK OP1 G A 7 CA CA A 102 1555 3555 2.34 LINK O2' A B 5 CA CA B 101 1555 3555 2.86 LINK CA CA A 102 O HOH A 208 1555 3555 2.51 LINK CA CA B 101 O HOH B 208 1555 2555 3.16 SITE 1 AC1 7 U A 4 HOH A 212 HOH A 214 HOH A 215 SITE 2 AC1 7 HOH B 216 HOH B 219 HOH B 220 SITE 1 AC2 2 G A 7 HOH A 208 SITE 1 AC3 1 A B 5 CRYST1 47.671 47.671 51.885 90.00 90.00 120.00 H 3 18 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 0.020977 0.012111 0.000000 0.00000 SCALE2 0.000000 0.024222 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019273 0.00000