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DNA POLYMERASE BETA (E.C.2.7.7.7)/DNA COMPLEX, SOAKED IN THE PRESENCE OF ZNCL2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9ICK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 THIS ENTRY DESCRIBES THE STRUCTURE THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 24 HOURS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150 MILLIMOLAR ZNCL2, 0.001 MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Crystal Properties Matthews coefficient Solvent content 3 59.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.512 α = 90 b = 57.726 β = 90 c = 48.522 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 AREA DETECTOR SDMS 1995-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 20 83 4.4 1.9 10762
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 62 14.4 1.5
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER 9ICK 2.8 20 10762 83 0.196 0.1864
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation t_dihedral_angle_d 24 t_it 6.7 t_angle_deg 2.8 t_nbd 0.025 t_bond_d 0.02 t_trig_c_planes 0.012 t_gen_planes 0.006 t_incorr_chiral_ct t_pseud_angle
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2623 Nucleic Acid Atoms 248 Solvent Atoms 150 Heterogen Atoms 2
Software Software Software Name Purpose TNT refinement SDMS data reduction SDMS data scaling TNT phasing