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Binary complex of human DNA polymerase beta with a gapped DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BPX PDB entry 1BPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291 50 mM Imidazole pH 7.5, 350 mM Sodium acetate, 18% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.39 48.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.38 α = 90 b = 79.24 β = 105.49 c = 54.88 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 92 Viramax 2006-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 50 99.3 0.13 6.7 1.9 30271 30271 -3 5.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2 2.07 96.8 0.557 2.1 1.9 2929
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1BPX 2 21.86 30271 27022 2728 89 0.211 0.211 0.213 0.271 0.2729 RANDOM 24
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] 1.9 1.48 -0.48 -1.42
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 24.3 c_scangle_it 2.93 c_mcangle_it 2.25 c_scbond_it 2.04 c_mcbond_it 1.42 c_angle_deg 1.1 c_improper_angle_d 0.96 c_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2593 Nucleic Acid Atoms 632 Solvent Atoms 554 Heterogen Atoms 9
Software Software Software Name Purpose HKL-2000 data collection CNS refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing