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X-ray radiation damage series on Proteinase K at 277K, crystal structure, dataset 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Proteinase K was dissolved at a final concentration of 30 mg/ml in 10mM Calcium Chloride, 50 mM Tris pH 7.5. 1-2 microliters of this protein solution was mixed with an equivalent volume of precipitant solution from the well (1.0 M Ammonium Sulfate).
Crystal Properties Matthews coefficient Solvent content 2.02 39.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.82 α = 90 b = 67.82 β = 90 c = 101.865 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 PIXEL DECTRIS PILATUS 6M 2018-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.88557 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.02 34.91 99.9 0.098 0.038 8.5 6.8 120801 8.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.02 1.04 98.3 1.72 0.862 0.9 4.9
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 FREE R-VALUE 1IC6 1.02 33.91 1.34 120584 5878 99.79 0.1235 0.1228 0.1228 0.1381 0.1384 11.81
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 12.8487 f_angle_d 0.9231 f_chiral_restr 0.0757 f_bond_d 0.0063 f_plane_restr 0.0062
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2032 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 16
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing