HEADER RNA 11-MAY-25 9OKY TITLE 16MER SELF-COMPLEMENTARY DUPLEX RNA WITH DG:S(2)C PAIR SEQUENCE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA (5'-R(*A)-D(P*G)- COMPND 3 R(P*AP*GP*AP*AP*GP*AP*UP*CP*UP*UP*CP*UP*(RSP)P*U)-3'); COMPND 4 CHAIN: A, B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630 KEYWDS DEOXYRIBO-PURINE, 2-THIOCYTIDINE, RNA DUPLEX, ORIGIN OF LIFE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR Z.FANG,J.W.SZOSTAK REVDAT 2 26-NOV-25 9OKY 1 JRNL REVDAT 1 22-OCT-25 9OKY 0 JRNL AUTH Z.FANG,O.ACIKGOZ,X.JIA,J.ESSEX,R.WEN,J.W.SZOSTAK JRNL TITL IMPACT OF 2'-DEOXYRIBO-PURINE SUBSTRATES ON NONENZYMATIC RNA JRNL TITL 2 TEMPLATE-DIRECTED PRIMER EXTENSION. JRNL REF NUCLEIC ACIDS RES. V. 53 2025 JRNL REFN ESSN 1362-4962 JRNL PMID 41261857 JRNL DOI 10.1093/NAR/GKAF1228 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.FANG,O.ACIKGOZ,X.JIA,J.ESSEX,R.WEN,J.W.SZOSTAK REMARK 1 TITL IMPACT OF 2'-DEOXYRIBO-PURINE SUBSTRATES ON NONENZYMATIC RNA REMARK 1 TITL 2 TEMPLATE-DIRECTED PRIMER EXTENSION. REMARK 1 REF BIORXIV 2025 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 40909494 REMARK 1 DOI 10.1101/2025.08.29.673048 REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.33 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4 REMARK 3 NUMBER OF REFLECTIONS : 15039 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.439 REMARK 3 FREE R VALUE TEST SET COUNT : 818 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 971 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.32 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 62 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 670 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 138 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.00300 REMARK 3 B22 (A**2) : -0.00300 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : -0.00200 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.055 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.456 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 748 ; 0.012 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 312 ; 0.002 ; 0.019 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1160 ; 2.212 ; 1.897 REMARK 3 BOND ANGLES OTHERS (DEGREES): 762 ; 0.719 ; 1.728 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 156 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 366 ; 0.022 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 118 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 77 ; 0.094 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 78 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 281 ; 0.251 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 101 ; 0.193 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 748 ; 1.542 ; 1.388 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 749 ; 1.541 ; 1.388 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1160 ; 2.236 ; 2.532 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1161 ; 2.235 ; 2.532 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9OKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-25. REMARK 100 THE DEPOSITION ID IS D_1000295001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-24 REMARK 200 TEMPERATURE (KELVIN) : 99 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97648 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15145 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.478 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.2000 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) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.50600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 2.0 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 21.71100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 12.53485 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 85.47900 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 21.71100 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 12.53485 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 85.47900 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 21.71100 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 12.53485 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 85.47900 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 21.71100 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 12.53485 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 85.47900 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 21.71100 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 12.53485 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 85.47900 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 21.71100 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 12.53485 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 85.47900 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 25.06970 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 170.95800 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 25.06970 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 170.95800 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 25.06970 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 170.95800 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 25.06970 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 170.95800 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 25.06970 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 170.95800 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 25.06970 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 170.95800 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 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 103 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 115 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 122 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 136 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 141 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 145 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 166 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 105 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 109 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 138 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 139 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 140 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 137 O HOH B 169 1.96 REMARK 500 O HOH B 106 O HOH B 159 2.11 REMARK 500 N7 A B 1 O HOH B 101 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 171 O HOH B 171 2565 1.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 G A 7 N1 - C6 - O6 ANGL. DEV. = 3.9 DEGREES REMARK 500 G A 7 C5 - C6 - O6 ANGL. DEV. = -4.5 DEGREES REMARK 500 U A 9 O3' - P - OP2 ANGL. DEV. = 7.8 DEGREES REMARK 500 U A 14 O3' - P - OP2 ANGL. DEV. = 7.2 DEGREES REMARK 500 RSP A 15 O3' - P - OP2 ANGL. DEV. = 8.1 DEGREES REMARK 500 G B 4 O5' - P - OP2 ANGL. DEV. = -6.4 DEGREES REMARK 500 U B 14 O3' - P - OP2 ANGL. DEV. = 9.3 DEGREES REMARK 500 RSP B 15 O3' - P - OP2 ANGL. DEV. = 7.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL DBREF 9OKY A 1 16 PDB 9OKY 9OKY 1 16 DBREF 9OKY B 1 16 PDB 9OKY 9OKY 1 16 SEQRES 1 A 16 A DG A G A A G A U C U U C SEQRES 2 A 16 U RSP U SEQRES 1 B 16 A DG A G A A G A U C U U C SEQRES 2 B 16 U RSP U HET RSP A 15 20 HET RSP B 15 20 HETNAM RSP 4-AMINO-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL) HETNAM 2 RSP PYRIMIDINE-2(1H)-THIONE FORMUL 1 RSP 2(C9 H14 N3 O7 P S) FORMUL 3 HOH *138(H2 O) LINK O3' U A 14 P RSP A 15 1555 1555 1.60 LINK O3' RSP A 15 P U A 16 1555 1555 1.61 LINK O3' U B 14 P RSP B 15 1555 1555 1.58 LINK O3' RSP B 15 P U B 16 1555 1555 1.61 CRYST1 43.422 43.422 256.437 90.00 90.00 120.00 H 3 2 36 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 0.023030 0.013296 0.000000 0.00000 SCALE2 0.000000 0.026593 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003900 0.00000 CONECT 284 296 CONECT 296 284 313 314 315 CONECT 297 298 304 305 CONECT 298 297 299 300 CONECT 299 298 CONECT 300 298 301 CONECT 301 300 302 303 CONECT 302 301 CONECT 303 301 304 CONECT 304 297 303 CONECT 305 297 306 311 CONECT 306 305 307 308 CONECT 307 306 CONECT 308 306 309 310 CONECT 309 308 316 CONECT 310 308 311 312 CONECT 311 305 310 CONECT 312 310 313 CONECT 313 296 312 CONECT 314 296 CONECT 315 296 CONECT 316 309 CONECT 620 632 CONECT 632 620 649 650 651 CONECT 633 634 640 641 CONECT 634 633 635 636 CONECT 635 634 CONECT 636 634 637 CONECT 637 636 638 639 CONECT 638 637 CONECT 639 637 640 CONECT 640 633 639 CONECT 641 633 642 647 CONECT 642 641 643 644 CONECT 643 642 CONECT 644 642 645 646 CONECT 645 644 652 CONECT 646 644 647 648 CONECT 647 641 646 CONECT 648 646 649 CONECT 649 632 648 CONECT 650 632 CONECT 651 632 CONECT 652 645 MASTER 375 0 2 0 0 0 0 6 808 2 44 4 END