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Crystal structure of human PCNA in complex with ZRANB3 APIM motif peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 100 mM lithium sulfate + 30% (w/v) polyvinylpyrrolidone + 100 mM HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.4 48.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.631 α = 90 b = 84.631 β = 90 c = 201.77 γ = 120
Symmetry Space Group P 31 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 PIXEL DECTRIS PILATUS 6M 2015-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 1.2822 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 73.29 100 0.104 0.998 15.1 11.2 31686
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.55 100 1.297 0.565 2 9.7
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 1VYM 2.45 73.29 30026 1605 100 0.22308 0.22093 0.2221 0.2642 0.2685 RANDOM 66.671
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] 2.44 1.22 2.44 -7.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.319 r_dihedral_angle_4_deg 20.167 r_dihedral_angle_3_deg 18.096 r_long_range_B_refined 10.599 r_long_range_B_other 10.529 r_dihedral_angle_1_deg 8.362 r_scangle_other 5.944 r_mcangle_other 5.712 r_mcangle_it 5.711 r_scbond_it 3.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 46.319 r_dihedral_angle_4_deg 20.167 r_dihedral_angle_3_deg 18.096 r_long_range_B_refined 10.599 r_long_range_B_other 10.529 r_dihedral_angle_1_deg 8.362 r_scangle_other 5.944 r_mcangle_other 5.712 r_mcangle_it 5.711 r_scbond_it 3.952 r_scbond_other 3.627 r_mcbond_it 3.491 r_mcbond_other 3.489 r_angle_refined_deg 1.42 r_angle_other_deg 0.995 r_chiral_restr 0.088 r_gen_planes_refined 0.012 r_bond_refined_d 0.011 r_gen_planes_other 0.008 r_bond_other_d 0.005 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 6055 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing