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Crystal structure of Staphylococcus aureus ketol-acid reductoisomerase in complex with Mg2+, and JK-5-115
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.1 293 0.2 M sodium acetate pH 8.1
35% PEG 3350
0.5 mM JK-5-115
3.5 mM MgCl2
3.5 mM NADPH
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.031 α = 90 b = 94.353 β = 90 c = 96.996 γ = 90
Symmetry Space Group P 21 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 EIGER X 16M 2021-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.97 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.73 48.5 98.5 0.056 10 10 19410 59.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.977 0.326
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 2.73 48.5 1.35 19410 1936 97.77 0.2219 0.2165 0.2165 0.2709 0.2721 62.35
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 15.0946 f_angle_d 0.8374 f_chiral_restr 0.0616 f_plane_restr 0.0061 f_bond_d 0.0047
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4770 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing