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Structure of a DNA retention-prone PCNA variant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 50 mM sodium citrate pH 5.3 and 1.7 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 5.06 75.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.716 α = 90 b = 121.716 β = 90 c = 121.716 γ = 90
Symmetry Space Group P 21 3
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 RIGAKU SATURN 944 2017-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
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 2.85 50 100 0.145 0.149 0.033 0.999 25.99 20.8 14213 55.95
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 2.85 2.9 100 1.072 1.102 0.256 0.858 2.35 18.8
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4YHR 2.85856959127 38.4899787685 1.33473444407 13611 689 95.8993870218 0.243790221328 0.242032540516 0.2417 0.275881391497 0.2725 Random selection 59.5193499882
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 3.31838842769 f_angle_d 0.83265260119 f_chiral_restr 0.0485084592907 f_bond_d 0.00604031018633 f_plane_restr 0.00491871153937
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2012 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose Coot model building PHENIX refinement PHASER phasing HKL-3000 data reduction HKL-3000 data scaling HKL-3000 data collection