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DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7) COMPLEXED WITH SEVEN BASE PAIRS OF DNA; SOAKED IN THE PRESENCE OF CSCL (150 MILLIMOLAR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZQG
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 7 BASE PAIRS OF DNA (SEE ENTRY 9ICJ AND REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 3 DAYS: PEG 3350, 16% IMIDAZOLE, 100 MILLIMOLAR, PH 6.5 CSCL, 150 MILLIMOLAR SEE REFERENCE 3 FOR DETAILS CONCERNING EXPERIMENTAL PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.
Crystal Properties Matthews coefficient Solvent content 3 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.892 α = 90 b = 57.773 β = 90 c = 48.395 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 1996-01-30 M
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 2.9 20 90 0.082 2 10554
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) 2.9 3 87 0.196 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-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION DIFFERENCE FOURIER 1ZQG 2.9 20 10554 90 0.183
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 23.9 t_it 6 t_angle_deg 2.8 t_nbd 0.034 t_bond_d 0.019 t_trig_c_planes 0.015 t_gen_planes 0.005 t_incorr_chiral_ct t_pseud_angle
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2623 Nucleic Acid Atoms 289 Solvent Atoms 142 Heterogen Atoms 2
Software Software Software Name Purpose TNT refinement SDMS data reduction SDMS data scaling TNT phasing