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Crystal structure of PCNA from Chaetomium thermophilum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TUP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 0.1M PTCP pH 5.0, 25% PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.26 45.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.27 α = 90 b = 86.27 β = 90 c = 90.842 γ = 120
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+ 2020-10-23 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 2.34 30.28 98.9 0.097 0.108 0.046 0.997 9.6 5.2 10552
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 2.34 2.42 90.7 0.547 0.637 0.32 0.786 3.7
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 5TUP 2.34 30.28 9986 544 98.96 0.2161 0.2127 0.2163 0.2798 0.282 RANDOM 45.245
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] 1.32 0.66 1.32 -4.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.243 r_dihedral_angle_4_deg 21.718 r_dihedral_angle_3_deg 16.683 r_dihedral_angle_1_deg 7.52 r_angle_refined_deg 1.444 r_angle_other_deg 1.184 r_chiral_restr 0.053 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.243 r_dihedral_angle_4_deg 21.718 r_dihedral_angle_3_deg 16.683 r_dihedral_angle_1_deg 7.52 r_angle_refined_deg 1.444 r_angle_other_deg 1.184 r_chiral_restr 0.053 r_bond_refined_d 0.006 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 1857 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction