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OvsA from Halomonas utahensis, an ovoselenol-biosynthetic selenoxide synthase in complex with histidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 0.1 M sodium acetate pH 4.8, 3.9 M sodium formate
Crystal Properties Matthews coefficient Solvent content 4.26 71.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.129 α = 90 b = 160.129 β = 90 c = 122.312 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2023-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
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 2.72 69.34 99.93 0.02925 0.04136 0.02925 0.999 16.89 2 47873 74.79
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 2.72 2.817 99.92 0.5307 0.7505 0.5307 0.654 1.5 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.72 69.34 1.34 47843 1967 99.94 0.2256 0.2247 0.2251 0.2463 0.2461 78.6
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 17.7385 f_angle_d 0.8775 f_chiral_restr 0.0552 f_plane_restr 0.0096 f_bond_d 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7168 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 32
Software Software Software Name Purpose PHENIX refinement Coot model building MOSFLM data reduction Aimless data scaling PHASER phasing