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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 VAPOR DIFFUSION, HANGING DROP 7.9 294 20% PEG3350, 0.2M lithium nitrate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.58 52.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.927 α = 90 b = 51.069 β = 98.08 c = 86.026 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE MAR scanner 345 mm plate 2005-05-04 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 1.92 30 93.8 0.043 16.8 3 30796 28887 -1 37.479
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 1.92 1.95 90.6 0.507 2.5 1393
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 1.92 20.35 -1 29312 27934 1217 100 0.207 0.207 0.205 0.2718 0.247 0.3081 RANDOM 46.44
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.645 r_dihedral_angle_4_deg 19.366 r_dihedral_angle_3_deg 17.554 r_dihedral_angle_1_deg 6.629 r_scangle_it 2.815 r_scbond_it 1.849 r_angle_refined_deg 1.427 r_mcangle_it 1.116 r_mcbond_it 0.738 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.645 r_dihedral_angle_4_deg 19.366 r_dihedral_angle_3_deg 17.554 r_dihedral_angle_1_deg 6.629 r_scangle_it 2.815 r_scbond_it 1.849 r_angle_refined_deg 1.427 r_mcangle_it 1.116 r_mcbond_it 0.738 r_nbtor_refined 0.303 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.175 r_symmetry_hbond_refined 0.169 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2701 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection PHASER phasing