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Complex structure of PCNA with UHRF2
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, SITTING DROP 289 2 M ammonium sulfate, 0.1 M Tris pH 8.0
Crystal Properties Matthews coefficient Solvent content 4.27 71.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 202.514 α = 90 b = 202.514 β = 90 c = 123.937 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 CCD ADSC QUANTUM 315r 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9791 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 50 98.1 0.051 0.067 0.043 12.1 2.1 94479 41.15
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 2.2 2.28 99.2 0.467 0.621 0.405 0.64 2.1
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 2.199 41.312 1.97 94464 4857 98.06 0.2048 0.2039 0.2045 0.2201 0.2222 48.4451
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 7.729 f_angle_d 1.298 f_chiral_restr 0.061 f_bond_d 0.01 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7806 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction