HEADER RNA 16-JUN-26 36LL TITLE 16MER SELF-COMPLEMENTARY RNA DUPLEX WITH L-U COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (16-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS NONENZYMATIC RNA REPLICATION, CHIRALITY, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.ESSEX,J.W.SZOSTAK REVDAT 1 01-JUL-26 36LL 0 JRNL AUTH J.ESSEX,X.JIA,J.ZHANG,J.W.SZOSTAK JRNL TITL EFFECTS OF CHEMICALLY ACTIVATED L-NUCLEOTIDES ON JRNL TITL 2 NONENZYMATIC RNA COPYING JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.8 REMARK 3 NUMBER OF REFLECTIONS : 8759 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 877 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 24.2700 - 2.4600 0.98 1573 175 0.1956 0.2061 REMARK 3 2 2.4500 - 1.9500 1.00 1521 170 0.2951 0.3191 REMARK 3 3 1.9500 - 1.7000 1.00 1504 168 0.2786 0.2736 REMARK 3 4 1.7000 - 1.5500 1.00 1482 164 0.3006 0.3371 REMARK 3 5 1.5500 - 1.4400 0.96 1431 159 0.3098 0.3188 REMARK 3 6 1.4400 - 1.3500 0.25 371 41 0.2927 0.4003 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.187 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.93 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 : 0.005 377 REMARK 3 ANGLE : 1.074 587 REMARK 3 CHIRALITY : 0.054 77 REMARK 3 PLANARITY : 0.010 21 REMARK 3 DIHEDRAL : 22.623 229 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 36LL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-26. REMARK 100 THE DEPOSITION ID IS D_1000309078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-DEC-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC 1.0.5 REMARK 200 DATA SCALING SOFTWARE : AUTOPROC 1.0.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8765 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 24.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.44 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.04 M LITHIUM CHLORIDE, 0.08 M REMARK 280 STRONTIUM CHLORIDE HEXAHYDRATE, 0.04 M SODIUM CACODYLATE REMARK 280 TRIHYDRATE PH 7.0, 30%V/V (+/-)-2-METHYL-2,4-PENTANEDIOL, 0.012 REMARK 280 M SPERMINE TETRAHYDROCHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 21.04550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 12.15063 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 43.37100 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 21.04550 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 12.15063 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 43.37100 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 21.04550 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 12.15063 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 43.37100 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 21.04550 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 12.15063 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 43.37100 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 21.04550 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 12.15063 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 43.37100 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 21.04550 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 12.15063 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 43.37100 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 24.30125 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 86.74200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 24.30125 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 86.74200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 24.30125 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 86.74200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 24.30125 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 86.74200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 24.30125 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 86.74200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 24.30125 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 86.74200 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: 1420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 121 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 125 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 131 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 138 LIES ON A SPECIAL POSITION. DBREF 36LL A 1 16 PDB 36LL 36LL 1 16 SEQRES 1 A 16 A G A G A LCA G A U C 0U U C SEQRES 2 A 16 U C U HET LCA A 6 23 HET 0U A 11 20 HETNAM LCA [(1R,3R,4R,7S)-7-HYDROXY-3-(ADENIN-9-YL)-2,5- HETNAM 2 LCA DIOXABICYCLO[2.2.1]HEPT-1-YL]METHYL DIHYDROGEN HETNAM 3 LCA PHOSPHATE HETNAM 0U L-URIDINE-5'-MONOPHOSPHATE FORMUL 1 LCA C11 H14 N5 O7 P FORMUL 1 0U C9 H13 N2 O9 P FORMUL 2 HOH *46(H2 O) LINK O3' A A 5 P LCA A 6 1555 1555 1.60 LINK O3' LCA A 6 P G A 7 1555 1555 1.61 LINK O3' C A 10 P 0U A 11 1555 1555 1.60 LINK O3' 0U A 11 P U A 12 1555 1555 1.60 CRYST1 42.091 42.091 130.113 90.00 90.00 120.00 H 3 2 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 0.023758 0.013717 0.000000 0.00000 SCALE2 0.000000 0.027433 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007686 0.00000 CONECT 96 110 CONECT 110 96 111 128 131 CONECT 111 110 112 CONECT 112 111 123 CONECT 113 121 123 130 CONECT 114 123 132 CONECT 115 116 117 124 CONECT 116 115 118 CONECT 117 115 119 129 CONECT 118 116 119 CONECT 119 117 118 120 CONECT 120 119 122 126 CONECT 121 113 124 132 CONECT 122 120 CONECT 123 112 113 114 127 CONECT 124 115 121 127 CONECT 125 126 129 CONECT 126 120 125 CONECT 127 123 124 CONECT 128 110 CONECT 129 117 125 CONECT 130 113 133 CONECT 131 110 CONECT 132 114 121 CONECT 133 130 CONECT 206 218 CONECT 218 206 219 220 221 CONECT 219 218 CONECT 220 218 CONECT 221 218 222 CONECT 222 221 223 CONECT 223 222 224 225 CONECT 224 223 229 CONECT 225 223 226 227 CONECT 226 225 238 CONECT 227 225 228 229 CONECT 228 227 CONECT 229 224 227 230 CONECT 230 229 231 237 CONECT 231 230 232 233 CONECT 232 231 CONECT 233 231 234 CONECT 234 233 235 236 CONECT 235 234 CONECT 236 234 237 CONECT 237 230 236 CONECT 238 226 MASTER 271 0 2 0 0 0 0 6 383 1 47 2 END