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Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary complex forms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JX4 PDB ENTRY 1JX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 294 10-15% PEG3350, 0.2M calcium acetate, 0.1M HEPES pH 7.0, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.7 54.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.993 α = 90 b = 102.51 β = 90 c = 106.109 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 2.2 30 97.5 0.055 18.1 2.8 53280 51948 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) 1 2.2 2.24 99.7 0.36 2.1 2513
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT PDB ENTRY 1JX4 2.2 24.11 2 51924 51924 2660 100 0.221 0.221 0.21 0.2368 0.256 0.2753 RANDOM 45.17
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] 2.55 -1.66 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.202 r_dihedral_angle_4_deg 16.448 r_dihedral_angle_3_deg 15.631 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.756 r_scbond_it 1.744 r_angle_refined_deg 1.502 r_mcangle_it 1.115 r_mcbond_it 0.678 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.202 r_dihedral_angle_4_deg 16.448 r_dihedral_angle_3_deg 15.631 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.756 r_scbond_it 1.744 r_angle_refined_deg 1.502 r_mcangle_it 1.115 r_mcbond_it 0.678 r_nbtor_refined 0.303 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.152 r_symmetry_vdw_refined 0.151 r_symmetry_hbond_refined 0.136 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5486 Nucleic Acid Atoms 1202 Solvent Atoms 305 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection