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X-ray radiation damage series on Proteinase K at 100K, crystal structure, dataset 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7LN7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Proteinase K was dissolved in 10 mM Calcium Chloride, 50 mM Tris pH 7.5 at a final concentration of 30 mg/ml. 1-2 microliters of this protein solution was mixed with an equivalent volume of precipitant solution (0.5 M Sodium Nitrate).
Crystal Properties Matthews coefficient Solvent content 2.01 38.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.721 α = 90 b = 67.721 β = 90 c = 101.423 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 100 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 0.9 34.82 99.6 0.076 0.029 10.3 6.9 173186 5.85
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 0.9 0.92 93 0.716 0.519 1 2.2
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 7LN7 0.9 33.86 1.34 173030 8457 99.56 0.1582 0.1574 0.172 0.1831 9.99
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 12.9486 f_angle_d 0.8993 f_chiral_restr 0.0744 f_plane_restr 0.0059 f_bond_d 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2032 Nucleic Acid Atoms Solvent Atoms 461 Heterogen Atoms 21
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing