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PCNA from Chaetomium thermophilum in complex with PolD4 PIP peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7O1E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate, pH 6.5, 36 % v/v PEG 300
Crystal Properties Matthews coefficient Solvent content 2.54 51.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.891 α = 60.94 b = 84.711 β = 89.6 c = 84.89 γ = 81.22
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 944+ 2020-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.45 30.39 94.2 0.13 0.151 0.076 0.994 7.2 3.9 59727
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.52 92.1 1.368 1.61 0.841 0.406 3.6
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 7O1E 2.45 30.39 56897 2829 94.16 0.2221 0.2202 0.226 0.2619 0.2667 RANDOM 43.964
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] 1.51 0.94 -2.29 1.3 0.95 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.16 r_dihedral_angle_4_deg 20.746 r_dihedral_angle_3_deg 16.553 r_dihedral_angle_1_deg 7.773 r_angle_refined_deg 1.461 r_angle_other_deg 1.226 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.16 r_dihedral_angle_4_deg 20.746 r_dihedral_angle_3_deg 16.553 r_dihedral_angle_1_deg 7.773 r_angle_refined_deg 1.461 r_angle_other_deg 1.226 r_chiral_restr 0.06 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11435 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction