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Bacillithiol Disulfide Reductase Bdr (YpdA) from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7A76
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.03 M magnesium chloride, 0.03 M calcium chloride, 0.1 M bicine/Trizma, pH = 8.5, 10% w/v PEG 4000, 20% v/v glycerol
Crystal Properties Matthews coefficient Solvent content 2.8 55.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.308 α = 90 b = 180.308 β = 90 c = 350.459 γ = 120
Symmetry Space Group P 61 2 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 EIGER X 16M 2019-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.946444 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.1 29.94 99.9 0.125 0.119 0.998 14.3 9.8 61638 63.11
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.18 99.9 0.505 0.48 0.938 4.5 10.3
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 7A76 3.1 29.94 1.34 61548 3106 99.95 0.2464 0.2441 0.2446 0.2908 0.291 68.73
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 20.0722 f_angle_d 0.65 f_chiral_restr 0.05 f_plane_restr 0.0036 f_bond_d 0.0025
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20137 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 568
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing