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DNA Polymerase Eta in Complex With a cis-syn Thymidine Dimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JIH PDB ENTRY 1JIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 33% PEG 4000, 0.1 M TRIS, 0.2 M Lithium Sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.087 α = 90 b = 226.962 β = 90 c = 85.919 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 315 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 1.0809 APS 24-ID-C
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 1.76 50 99.8 0.129 10.5 7.2 85689 85518
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) 1.76 1.82 99.6 0.665 6.9
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 1JIH 1.76 35 85732 81185 4273 99.68 0.16475 0.16354 0.183 0.18721 0.2055 RANDOM 21.038
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] 0.23 -0.31 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.678 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 12.731 r_dihedral_angle_1_deg 5.862 r_scangle_it 3.315 r_scbond_it 2.106 r_angle_refined_deg 1.59 r_mcangle_it 1.39 r_angle_other_deg 0.902 r_mcbond_it 0.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.678 r_dihedral_angle_4_deg 20.581 r_dihedral_angle_3_deg 12.731 r_dihedral_angle_1_deg 5.862 r_scangle_it 3.315 r_scbond_it 2.106 r_angle_refined_deg 1.59 r_mcangle_it 1.39 r_angle_other_deg 0.902 r_mcbond_it 0.714 r_mcbond_other 0.178 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 4035 Nucleic Acid Atoms 508 Solvent Atoms 709 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection PHASER phasing