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Human DNA polymerase kappa extending opposite a cis-syn thymine dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OH2 PDB ENTRY 2OH2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 14% PEG 5000 monomethylether, 0.2M potassium acetate, 0.1M sodium chloride, 0.1M sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.61 65.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.136 α = 90 b = 154.476 β = 90 c = 217.854 γ = 90
Symmetry Space Group C 2 2 21
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 ADSC QUANTUM 210 2008-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97949 APS 17-ID
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 3.23 50 99.4 0.112 13.7 4.8 31785 31594
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) 1 3.23 3.35 95.3 0.866 4.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2OH2 3.336 46.67 27432 1452 99.16 0.24389 0.24165 0.2445 0.28778 0.288 RANDOM 97.177
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] 0.81 8.43 -9.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.604 r_dihedral_angle_3_deg 19.574 r_dihedral_angle_4_deg 18.409 r_dihedral_angle_1_deg 6.526 r_angle_refined_deg 1.681 r_scangle_it 1.64 r_angle_other_deg 0.976 r_scbond_it 0.9 r_mcangle_it 0.583 r_mcbond_it 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.604 r_dihedral_angle_3_deg 19.574 r_dihedral_angle_4_deg 18.409 r_dihedral_angle_1_deg 6.526 r_angle_refined_deg 1.681 r_scangle_it 1.64 r_angle_other_deg 0.976 r_scbond_it 0.9 r_mcangle_it 0.583 r_mcbond_it 0.303 r_chiral_restr 0.094 r_mcbond_other 0.04 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6544 Nucleic Acid Atoms 1127 Solvent Atoms 8 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing