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Crystal Structure Analysis of human PRPK complex with a compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ENP 3ENP, 4WW5 experimental model PDB 4WW5 3ENP, 4WW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 293 100mM Sodium citrate pH 5.2, 12.8% PEG8000, 10mM MgCl2, 10mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.25 45.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 295.77 α = 90 b = 47.63 β = 96.77 c = 62.14 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9792 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.02 61.71 99.6 0.091 0.047 14.3 3.7 56764 27.293
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.02 2.05 100 1.094 0.562 1.6 3.7
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 THROUGHOUT 3ENP, 4WW5 2.02 61.707 1.34 56754 2890 99.58 0.1718 0.1698 0.1708 0.209 0.2101 37.3591
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 6.101 f_angle_d 1.328 f_chiral_restr 0.067 f_bond_d 0.014 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6222 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 76
Software Software Software Name Purpose xia2 data scaling PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction PHASER phasing