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Crystal structure of the Aeropyrum pernix PCNA2 homotrimer
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GE8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 0.1 M citric acid, 1.8 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 3.56 65.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.788 α = 90 b = 169.788 β = 90 c = 169.788 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 JUPITER 210 2006-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.00000 SPring-8 BL38B1
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 2.17 47.09 99.96 0.09542 0.09806 0.02247 0.999 24.82 18.8 167217 33.23
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 2.17 2.25 100 0.6612 0.6856 0.1801 0.933 4.23 14.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.17 47.09 0.03 167217 4241 99.97 0.2063 0.2047 0.207 0.2366 0.2381 39.34
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 19.1154 f_angle_d 0.7149 f_chiral_restr 0.0485 f_plane_restr 0.0059 f_bond_d 0.0048
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7969 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 60
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing