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Crystal structure of 3-isopropylmalate dehydrogenase from Burkholderia thailandensis in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IWH apo structure, 4iwh
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 Microlytics MCSG1 B7: 25.5% PEG 4000, 15% glycerol, 170mM Ammonium acetate; ButhA.00092.a.B1.PS0xxxx at 12.64 mg/ml; the drop was overlayed with 5ul 5mM NAD in reservoir and soaked over night; cryo: direct; tray 257491b7, puck tiz0-3
Crystal Properties Matthews coefficient Solvent content 2.6 52.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 144.35 α = 90 b = 60.9 β = 117.85 c = 105.05 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 CCD RIGAKU SATURN 944+ 2015-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.7 50 96.8 0.043 0.046 30.23 7.1 86107 -3 13.32
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 85.6 0.286 0.336 4.18 3.4
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 apo structure, 4iwh 1.7 43.612 1.34 86097 2000 96.94 0.1495 0.149 0.1499 0.1738 0.1748 Random selection 15.7571
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 13.282 f_angle_d 1.325 f_chiral_restr 0.067 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5356 Nucleic Acid Atoms Solvent Atoms 975 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction PHENIX refinement PDB_EXTRACT data extraction XSCALE data scaling PHENIX phasing