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Structure of pseudoprotease CspC from Clostridioides difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I0W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 294 0.2M MES pH 6.5 with 2.5 M ammonium chloride and 0.5 M guanidinium hydrochloride mixed equal volume with 22 mg/ml protein and equilibrated over 2M sodium chloride
Crystal Properties Matthews coefficient Solvent content 2.53 51.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.651 α = 90 b = 155.176 β = 90 c = 91.675 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 PIXEL DECTRIS PILATUS3 6M mirrors 2017-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.55 50 99.6 0.056 0.067 0.035 5.4 3.4 177295 17.87
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 1.55 1.61 97.7 0.595 0.716 0.394 0.749 3.1
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 4I0W 1.55 45.837 1.34 176693 17715 99.6 0.166 0.1638 0.1679 0.1864 0.1912 28.1374
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4159 Nucleic Acid Atoms Solvent Atoms 375 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction