3EZ4

Crystal structure of 3-methyl-2-oxobutanoate hydroxymethyltransferase from Burkholderia pseudomallei


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1M3Updb entry 1M3U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5289PACT 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 coefficientSolvent content
2.3848.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 173.784α = 90
b = 187.556β = 90
c = 83.493γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002008-08-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.97934APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.15098.50.10713.4614.6157415
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.12.18960.4652.34.315125

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1M3U2.138.55157130788698.320.1970.1950.244RANDOM23.973
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]
-0.070.08-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.304
r_dihedral_angle_4_deg23.162
r_dihedral_angle_3_deg15.926
r_dihedral_angle_1_deg10.638
r_scangle_it5.035
r_scbond_it3.028
r_mcangle_it1.802
r_angle_refined_deg1.752
r_angle_other_deg1.028
r_mcbond_it0.977
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.304
r_dihedral_angle_4_deg23.162
r_dihedral_angle_3_deg15.926
r_dihedral_angle_1_deg10.638
r_scangle_it5.035
r_scbond_it3.028
r_mcangle_it1.802
r_angle_refined_deg1.752
r_angle_other_deg1.028
r_mcbond_it0.977
r_mcbond_other0.254
r_chiral_restr0.103
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17895
Nucleic Acid Atoms
Solvent Atoms1447
Heterogen Atoms40

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling