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Crystal structure of a staphylococcal orthologue of CYP134A1 (CYPX) in complex with a heme-coordinated fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7OW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 0.15M Lithium sulfate, 0.05M Magnesium chloride hexahydrate, 0.1M HEPES pH 7.8, 20% v/v PEG Smear High
Crystal Properties Matthews coefficient Solvent content 2.53 51.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.154 α = 90 b = 108.574 β = 90 c = 105.768 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 EIGER2 XE 16M 2020-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.85 55.38 100 0.111 0.115 0.032 0.999 12.6 13.1 40202 30.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 100 2 0.785 0.793 1.1 13.4
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 7OW9 1.85 55.38 1.33 40038 2042 99.66 0.2069 0.2058 0.2084 0.2279 0.233 45.55
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 6.9776 f_angle_d 0.4995 f_chiral_restr 0.0379 f_plane_restr 0.0044 f_bond_d 0.0028
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3165 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing