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Crystal structure of Oryza sativa ketol-acid reductoisomerase in complex with Mg2+, and JK-5-114
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FR7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2 M NH4SO4 (Salt)
0.1 M BIS-TRIS 6.5 pH (Buffer)
25 %w/v PEG 3350 (Precipitant)
Crystal Properties Matthews coefficient Solvent content 2.16 42.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.41 α = 90 b = 91.863 β = 101.37 c = 86.998 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 R 1M 2024-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 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 1.96 46.01 97.8 0.035 9.9 6.8 473997 37.92
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 1.96 2 79.8 0.566
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 1.96 45.93 1.34 69154 2000 99.45 0.2135 0.2128 0.2145 0.238 0.2408 45.64
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 16.8287 f_angle_d 0.6636 f_chiral_restr 0.0419 f_plane_restr 0.0054 f_bond_d 0.0046
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7347 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 40
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHENIX phasing