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PCNA from Chaetomium thermophilum in complex with PolD3 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, SITTING DROP 4.2 293 0.1 M Phosphate/citrate, pH4.2, 40% v/v PEG300
Crystal Properties Matthews coefficient Solvent content 2.22 44.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.84 α = 90.93 b = 56.391 β = 90.55 c = 62.86 γ = 99.48
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+ mirrors 2023-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 27.57 93.2 0.091 0.113 0.067 0.988 5.7 2.6 25893
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 2.55 91 0.255 0.324 0.197 0.881 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.45 27.57 24703 1189 93.18 0.2144 0.21283 0.2178 0.24943 0.2527 RANDOM 30.35
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] -0.72 1.12 -0.18 0.06 0.05 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.267 r_dihedral_angle_1_deg 7.036 r_dihedral_angle_2_deg 3.67 r_long_range_B_refined 3.003 r_long_range_B_other 2.983 r_scangle_other 1.579 r_mcangle_other 1.361 r_mcangle_it 1.36 r_angle_refined_deg 0.962 r_scbond_it 0.932
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.267 r_dihedral_angle_1_deg 7.036 r_dihedral_angle_2_deg 3.67 r_long_range_B_refined 3.003 r_long_range_B_other 2.983 r_scangle_other 1.579 r_mcangle_other 1.361 r_mcangle_it 1.36 r_angle_refined_deg 0.962 r_scbond_it 0.932 r_scbond_other 0.931 r_mcbond_it 0.803 r_mcbond_other 0.803 r_angle_other_deg 0.34 r_chiral_restr 0.046 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5694 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Aimless data scaling iMOSFLM data reduction MOLREP phasing