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Crystal Structure analysis of PCNA from Thermococcus kodakaraensis tk0582
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 295 2.4-2.8 M ammonium sulfate, 100 mM sodium citrate, 5-10% 2,4-methyl pentanediol. The protein solution has 10% glycerol, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.89 57.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.48 α = 90 b = 136.27 β = 90 c = 123.97 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2009-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.4 29.86 90.8 0.039 13.4 2.83 36454
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 2.4 2.49 89 0.345 2.7 2.72 3505
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.4 29.63 35927 1798 89.49 0.246 0.243 0.2355 0.305 0.2909 RANDOM 57.023
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] 1.69 -2.28 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.905 r_dihedral_angle_4_deg 22.152 r_dihedral_angle_3_deg 19.45 r_dihedral_angle_1_deg 7.168 r_scangle_it 4.295 r_scbond_it 2.559 r_mcangle_it 1.803 r_angle_refined_deg 1.796 r_mcbond_it 0.965 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.905 r_dihedral_angle_4_deg 22.152 r_dihedral_angle_3_deg 19.45 r_dihedral_angle_1_deg 7.168 r_scangle_it 4.295 r_scbond_it 2.559 r_mcangle_it 1.803 r_angle_refined_deg 1.796 r_mcbond_it 0.965 r_chiral_restr 0.117 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5851 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 30
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction