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Crystal structure of human PCNA in complex with REV1 PIP-box
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZVM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.221 α = 90 b = 72.508 β = 90 c = 83.599 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2021-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
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 2.7 48.41 99.9 0.078 17.1 6.5 24928
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 2.7 2.85 0.82
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 2.7 43.77 23659 1230 99.89 0.21647 0.21413 0.2145 0.26057 0.26 RANDOM 67.13
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] -1.18 -2.15 3.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.142 r_long_range_B_refined 7.541 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 6.606 r_scangle_other 5.309 r_mcangle_it 4.33 r_mcangle_other 4.329 r_scbond_it 3.267 r_scbond_other 3.266 r_dihedral_angle_2_deg 2.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.142 r_long_range_B_refined 7.541 r_long_range_B_other 7.541 r_dihedral_angle_1_deg 6.606 r_scangle_other 5.309 r_mcangle_it 4.33 r_mcangle_other 4.329 r_scbond_it 3.267 r_scbond_other 3.266 r_dihedral_angle_2_deg 2.955 r_mcbond_it 2.639 r_mcbond_other 2.639 r_angle_refined_deg 1.349 r_angle_other_deg 0.573 r_chiral_restr 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_bond_other_d 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 5910 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing