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Crystal structure of OxdB E85A in complex with Z-2- (3-bromophenyl) propanal oxime
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 30% (w/v) polyethylene glycol 4,000, 0.1 M Tris pH8.5, and 0.2 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.19 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.922 α = 90 b = 64.685 β = 90.49 c = 52.563 γ = 90
Symmetry Space Group P 1 21 1
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 2020-04-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.91939 SPring-8 BL44XU
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 40.792 99.73 0.05767 0.06835 0.03633 0.999 14.41 3.5 22681 31.84
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 2.07 99.87 0.5143 0.6058 0.3174 0.827 2.32 3.6
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3a15 2 40.792 1.36 22675 2063 96.83 0.1855 0.1839 0.1859 0.2168 0.218 Random selection
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 14.952 f_angle_d 0.908 f_chiral_restr 0.054 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2691 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction