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Crystal Structure of Yeast Proliferating Cell Nuclear Antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein solution: 15 mg/mL protein in 20 mM HEPES and 150 mM NaCL at pH 7.5. Crystallization solution: 2.2M ammonium sulfate, 0.2M ammonium fluoride. Hanging drop was 50% protein solution, 50% crystallization solution
Crystal Properties Matthews coefficient Solvent content 5.32 76.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.259 α = 90 b = 124.259 β = 90 c = 124.259 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 NOIR-1 2013-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
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 2.95 37.47 100 0.109 12.2 21.82 13746 122.12
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 2.95 3.06 100 0.893 2.1 22.26 1358
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1PLQ 2.9502 37.465 1.33 13711 687 99.75 0.2477 0.2464 0.2733 0.2794 136.8029
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 12.302 f_angle_d 0.71 f_chiral_restr 0.025 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2011 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose d*TREK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction Coot model building