HEADER RNA 18-AUG-15 5D99 TITLE 3DW4 REDETERMINED BY DIRECT METHODS STARTING FROM RANDOM PHASE ANGLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (27-MER) HAIRPIN FROM SARCIN-RICIN DOMAIN OF E. COLI COMPND 3 23S RRNA; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE L1; SOURCE 4 ORGANISM_TAXID: 268588 KEYWDS AB INITIO DIRECT METHODS STRUCTURE DETERMINATION, HAIRPIN RNA, RNA EXPDTA X-RAY DIFFRACTION AUTHOR B.H.M.MOOERS REVDAT 6 06-MAR-24 5D99 1 REMARK REVDAT 5 25-DEC-19 5D99 1 JRNL REVDAT 4 11-DEC-19 5D99 1 REMARK REVDAT 3 27-SEP-17 5D99 1 REMARK REVDAT 2 15-MAR-17 5D99 1 TITLE REMARK REVDAT 1 13-APR-16 5D99 0 JRNL AUTH B.H.MOOERS JRNL TITL DIRECT-METHODS STRUCTURE DETERMINATION OF A TRYPANOSOME JRNL TITL 2 RNA-EDITING SUBSTRATE FRAGMENT WITH TRANSLATIONAL JRNL TITL 3 PSEUDOSYMMETRY. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 72 477 2016 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 27050127 JRNL DOI 10.1107/S2059798316001224 REMARK 0 REMARK 0 THIS ENTRY 5D99 REFLECTS AN ALTERNATIVE MODELING OF THE REMARK 0 STRUCTURAL DATA IN R3DW4SF ORIGINAL DATA DETERMINED BY AUTHOR: REMARK 0 V.OLIERIC,U.RIEDER,K.LANG,A.SERGANOV,C.SCHULZE-BRIESE,R.MICURA, REMARK 0 P.DUMAS,E.ENNIFAR REMARK 0 ORIGINAL DATA REFERENCE 1 REMARK 0 PDB ID: 3DW4 REMARK 0 AUTH V.OLIERIC,U.RIEDER,K.LANG,A.SERGANOV,C.SCHULZE-BRIESE, REMARK 0 AUTH 2 R.MICURA,P.DUMAS,E.ENNIFAR REMARK 0 TITL A FAST SELENIUM DERIVATIZATION STRATEGY FOR CRYSTALLIZATION REMARK 0 TITL 2 AND PHASING OF RNA STRUCTURES. REMARK 0 REF RNA V. 15 707 2009 REMARK 0 REFN ESSN 1469-9001 REMARK 0 PMID 19228585 REMARK 0 DOI 10.1261/RNA.1499309 REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2142 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38814 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.105 REMARK 3 R VALUE (WORKING SET) : 0.105 REMARK 3 FREE R VALUE : 0.120 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.230 REMARK 3 FREE R VALUE TEST SET COUNT : 2029 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 20.9565 - 2.3369 1.00 2665 149 0.1019 0.1215 REMARK 3 2 2.3369 - 1.8553 1.00 2622 150 0.1132 0.1230 REMARK 3 3 1.8553 - 1.6208 1.00 2629 147 0.0956 0.1099 REMARK 3 4 1.6208 - 1.4727 1.00 2628 146 0.0988 0.1123 REMARK 3 5 1.4727 - 1.3672 1.00 2640 131 0.1038 0.1280 REMARK 3 6 1.3672 - 1.2866 1.00 2595 163 0.0981 0.1118 REMARK 3 7 1.2866 - 1.2221 1.00 2671 136 0.0914 0.1066 REMARK 3 8 1.2221 - 1.1689 1.00 2597 158 0.0949 0.1092 REMARK 3 9 1.1689 - 1.1239 1.00 2618 131 0.1000 0.1188 REMARK 3 10 1.1239 - 1.0852 1.00 2609 152 0.1060 0.1160 REMARK 3 11 1.0852 - 1.0512 1.00 2614 136 0.1129 0.1250 REMARK 3 12 1.0512 - 1.0212 1.00 2603 151 0.1273 0.1302 REMARK 3 13 1.0212 - 0.9943 1.00 2650 138 0.1519 0.1635 REMARK 3 14 0.9943 - 0.9700 0.99 2644 141 0.1808 0.1912 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) : 0.060 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 10.590 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 : 0.006 758 REMARK 3 ANGLE : 1.224 1184 REMARK 3 CHIRALITY : 0.050 153 REMARK 3 PLANARITY : 0.020 31 REMARK 3 DIHEDRAL : 15.737 376 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 5D99 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: AB INITIO PHASING REMARK 200 SOFTWARE USED: SIR2014 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 3DW4. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 38.16500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.24750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 19.08250 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 HO2' U A 2653 HO2 GOL A 2701 1.29 REMARK 500 O HOH A 2828 O HOH A 2900 2.14 REMARK 500 OP2 A A 2670 O HOH A 2801 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2972 DISTANCE = 6.05 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 2701 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DW4 RELATED DB: PDB REMARK 900 3DW4 CONTAINS THE ORIGINAL STRUCTURE THAT WAS DETERMINED BY REMARK 900 MOLECULAR REPLACEMENT. THE CURRENT DEPOSITION IS A REDETERMINATION REMARK 900 OF THAT STRUCTURE BY DIRECT METHODS.THIS ENTRY 5D99 REFLECTS AN REMARK 900 ALTERNATIVE MODELING OF X-RAY DATA R3DW4SF DBREF 5D99 A 2647 2673 PDB 5D99 5D99 2647 2673 SEQRES 1 A 27 U G C OMU C C U A G U A C G SEQRES 2 A 27 A G A G G A C C G G A G U SEQRES 3 A 27 G HET OMU A2650 31 HET GOL A2701 14 HETNAM OMU O2'-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 OMU C10 H15 N2 O9 P FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *172(H2 O) LINK O3' C A2649 P OMU A2650 1555 1555 1.60 LINK O3' OMU A2650 P C A2651 1555 1555 1.60 SITE 1 AC1 9 U A2647 U A2653 A A2654 U A2656 SITE 2 AC1 9 A A2660 C A2666 HOH A2828 HOH A2922 SITE 3 AC1 9 HOH A2970 CRYST1 29.630 29.630 76.330 90.00 90.00 90.00 P 43 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 0.033750 0.000000 0.000000 0.00000 SCALE2 0.000000 0.033750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013101 0.00000