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Crystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 14% (w/v) polyethylene glycol (PEG) 3350, 100 mM potassium chloride, and 100 mM HEPES pH 7.5. Cryoprotectant contained 15% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.74 55.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.346 α = 90 b = 341.655 β = 107.14 c = 122.605 γ = 90
Symmetry Space Group P 1 21 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 2015-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.9795 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.048 50 99 0.168 0.99 8.4 7.07 486251
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 98.3 0.757 0.588 1.82 7.01
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 5FAU 2.05 49.817 1.35 486153 24248 98.81 0.1685 0.1672 0.1682 0.1949 0.1961 21.0358
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 21.812 f_angle_d 0.956 f_chiral_restr 0.082 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 50048 Nucleic Acid Atoms Solvent Atoms 4815 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling PHASER phasing