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Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M3U pdb entry 1M3U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 PACT screen condition H11, 0.1 M BisTris propane, 20% PEG 3350, 0.2 M Na Citrate, 0.4/0.4 uL drops, 24.4 mg/mL protein, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.38 48.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 173.784 α = 90 b = 187.556 β = 90 c = 83.493 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2008-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97934 APS 23-ID-D
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 2.1 50 98.5 0.107 13.461 4.6 157415
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) 2.1 2.18 96 0.465 2.3 4.3 15125
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1M3U 2.1 38.55 157130 7886 98.32 0.197 0.195 0.1952 0.244 0.2416 RANDOM 23.973
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] -0.07 0.08 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.304 r_dihedral_angle_4_deg 23.162 r_dihedral_angle_3_deg 15.926 r_dihedral_angle_1_deg 10.638 r_scangle_it 5.035 r_scbond_it 3.028 r_mcangle_it 1.802 r_angle_refined_deg 1.752 r_angle_other_deg 1.028 r_mcbond_it 0.977
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.304 r_dihedral_angle_4_deg 23.162 r_dihedral_angle_3_deg 15.926 r_dihedral_angle_1_deg 10.638 r_scangle_it 5.035 r_scbond_it 3.028 r_mcangle_it 1.802 r_angle_refined_deg 1.752 r_angle_other_deg 1.028 r_mcbond_it 0.977 r_mcbond_other 0.254 r_chiral_restr 0.103 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17895 Nucleic Acid Atoms Solvent Atoms 1447 Heterogen Atoms 40
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling