3EZ4

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

X-RAY DIFFRACTION

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	R-Free	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	0.244	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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.