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Crystal structure of human PCNA in complex with ZRANB3 PIP box 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 293 100 mM NaCl + 8% (v/v) DMSO + 31% pentaerythitol propoxylate (5/4 PO/OH)
Crystal Properties Matthews coefficient Solvent content 2.52 51.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.136 α = 90 b = 86.802 β = 90 c = 156.679 γ = 90
Symmetry Space Group P 21 21 21
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-F 2016-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.1402 Diamond I04
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 1.96 78.34 100 0.084 0.999 20.2 13 67566
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 1.96 2.01 100 1.763 0.566 1.5 13
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 1.96 78.34 64155 3325 99.95 0.21363 0.21129 0.2166 0.25933 0.2636 RANDOM 44.945
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] -0.27 -2.22 2.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.647 r_dihedral_angle_4_deg 16.818 r_dihedral_angle_3_deg 15.252 r_long_range_B_refined 8.498 r_long_range_B_other 8.404 r_dihedral_angle_1_deg 7.255 r_scangle_other 4.617 r_mcangle_it 3.904 r_mcangle_other 3.904 r_scbond_it 2.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.647 r_dihedral_angle_4_deg 16.818 r_dihedral_angle_3_deg 15.252 r_long_range_B_refined 8.498 r_long_range_B_other 8.404 r_dihedral_angle_1_deg 7.255 r_scangle_other 4.617 r_mcangle_it 3.904 r_mcangle_other 3.904 r_scbond_it 2.855 r_scbond_other 2.855 r_mcbond_it 2.452 r_mcbond_other 2.45 r_angle_refined_deg 1.401 r_angle_other_deg 1.091 r_chiral_restr 0.097 r_gen_planes_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_other 0.007 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 6175 Nucleic Acid Atoms Solvent Atoms 385 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing