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Crystal Structure of Yeast PCNA in Complex with N24 Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6B8I 6B8I, 5DA7 experimental model PDB 5DA7 6B8I, 5DA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 n-Octyl-b-D-glu, NaCi pH 5.5, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.82 61.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.35 α = 90 b = 84.03 β = 93.62 c = 58.15 γ = 90
Symmetry Space Group C 1 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 EIGER X 16M 2018-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.979 SSRF BL17U1
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 2.83 58.03 98.7 0.133 6.9 9212
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 2.83 2.9 99.4 0.512 7.2
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 6B8I, 5DA7 2.82 58.03 8684 527 98.4 0.3301 0.326 0.3156 0.3966 0.3689 RANDOM 99.825
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] 67.58 114.5 -81.24 13.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.033 r_dihedral_angle_4_deg 22.145 r_dihedral_angle_3_deg 20.118 r_dihedral_angle_1_deg 8.837 r_mcangle_it 5.734 r_mcbond_it 3.493 r_mcbond_other 3.49 r_angle_other_deg 1.392 r_angle_refined_deg 1.063 r_chiral_restr 0.043
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.033 r_dihedral_angle_4_deg 22.145 r_dihedral_angle_3_deg 20.118 r_dihedral_angle_1_deg 8.837 r_mcangle_it 5.734 r_mcbond_it 3.493 r_mcbond_other 3.49 r_angle_other_deg 1.392 r_angle_refined_deg 1.063 r_chiral_restr 0.043 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2155 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection PDB_EXTRACT data extraction XDS data reduction Aimless data scaling