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Crystal structure of a novel disulfide oxidoreductase from Deinococcus radiodurans crystallized in presence of beta-mercaptoethanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CNW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 PEG 8000, Glycerol, Sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.27 45.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.856 α = 90 b = 62.35 β = 90 c = 86.666 γ = 90
Symmetry Space Group P 21 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 CCD OXFORD TITAN CCD 2014-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 15.77 99.6 0.073 15.9 4.9 24630
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 98.2 0.551 1.9 2.7
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 5CNW 1.801 14.97 1.34 24554 1255 99.65 0.1763 0.1741 0.1784 0.2176 0.218 27.9995
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 13.828 f_angle_d 0.877 f_chiral_restr 0.039 f_bond_d 0.007 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1771 Nucleic Acid Atoms Solvent Atoms 228 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction CrysalisPro data processing Aimless data scaling PHASER phasing CrysalisPro data reduction