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Bacillithiol Disulfide Reductase Bdr (YpdA) from Bacillus cereus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other 3.5 A SELENO-SAD BCYPDA MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris, pH = 7.0, 10% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.26 45.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.731 α = 90 b = 114.9 β = 90 c = 146.73 γ = 90
Symmetry Space Group P 2 21 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 PILATUS 6M 2015-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97242 ESRF ID23-1
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 1.65 73.4 97.8 0.076 0.086 0.989 10 4.5 175671 27.09
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 1.65 1.68 96.3 0.81 0.915 0.728 4.7
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 3.5 A SELENO-SAD BCYPDA MODEL 1.65 45.23 1.33 175557 8787 97.49 0.1912 0.1898 0.1921 0.2182 0.2204 41.52
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 15.7002 f_angle_d 0.8171 f_chiral_restr 0.0584 f_bond_d 0.0061 f_plane_restr 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10276 Nucleic Acid Atoms Solvent Atoms 857 Heterogen Atoms 216
Software Software Software Name Purpose PHENIX refinement REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing