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Co-crystal structure of caPCNA bound to the AOH1996 derivative, AOH1996-1LE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VKX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1 M sodium cacodylate pH 6.5, 0.2 M sodium chloride, 2.0 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 4.29 71.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 199.492 α = 90 b = 199.492 β = 90 c = 129.413 γ = 120
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 2022-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9795 SSRL BL9-2
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 3.77 39.59 99.6 0.202 0.221 0.09 0.993 6.9 5.9 19342
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 3.77 4.13 99.1 0.788 0.862 0.347 0.774 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3VKX 3.77 39.59 1.96 19329 1895 99.6 0.2105 0.2051 0.2047 0.26 0.2568
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.102 f_angle_d 0.687 f_chiral_restr 0.049 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7341 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 230
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing