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Crystal structure of a 3-isopropylmalate dehydrogenase from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A05 PDB ENTRY 1A05
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 ButhA.00092.a.B1 PS01671 at 23.6 mg/mL against MCSG1 screen condition d3, 0.2 M MgCl2, 0.1 M TrisHCl pH 8.5, 30% PEG 400, crystal tracking ID 240482d3, unique puck ID quk9-15, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.57 52.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.6 α = 90 b = 60.1 β = 112.86 c = 103.19 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 CCD ADSC QUANTUM 315r 2013-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 1.283574 SSRL BL7-1
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 1.75 50 98.8 0.037 24.19 79884 -3 29.078
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 1.75 1.8 95.8 0.26 4.64
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1A05 1.75 19.63 79883 4014 98.87 0.1693 0.1676 0.201 0.2059 RANDOM 23.4711
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] 0.92 -0.36 0.18 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_4_deg 16.973 r_dihedral_angle_3_deg 12.157 r_dihedral_angle_1_deg 5.656 r_mcangle_it 1.551 r_angle_refined_deg 1.408 r_mcbond_it 1.023 r_mcbond_other 1.02 r_angle_other_deg 0.807 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.413 r_dihedral_angle_4_deg 16.973 r_dihedral_angle_3_deg 12.157 r_dihedral_angle_1_deg 5.656 r_mcangle_it 1.551 r_angle_refined_deg 1.408 r_mcbond_it 1.023 r_mcbond_other 1.02 r_angle_other_deg 0.807 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5339 Nucleic Acid Atoms Solvent Atoms 799 Heterogen Atoms 2
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction