3EON

2.55A crystal structure of native glutaryl-coa dehydrogenase from Burkholderia pseudomallei in complex with a small molecule

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	289	20% PEG 3000, 0.1M HEPES pH 7.5, 0.2M NaCl, VAPOR DIFFUSION, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.409	α = 90
b = 106.169	β = 90
c = 144.185	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARMOSAIC 300 mm CCD	ADJUSTABLE FOCUSING MIRRORS	2008-01-01		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.00	APS	21-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	2.4	50	100	0.118	16.981	7.2		59702

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	2.4	2.49	99.8		0.894		5.9	5874

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.55	46.63	49412	49412	2476	99.96	0.191	0.191	0.187	0.266	RANDOM	42.601

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]
0.22			-0.14		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.338
r_dihedral_angle_4_deg	21.668
r_dihedral_angle_3_deg	18.362
r_dihedral_angle_1_deg	6.004
r_scangle_it	2.7
r_scbond_it	1.714
r_angle_refined_deg	1.447
r_mcangle_it	1.303
r_mcbond_it	0.747
r_nbtor_refined	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.338
r_dihedral_angle_4_deg	21.668
r_dihedral_angle_3_deg	18.362
r_dihedral_angle_1_deg	6.004
r_scangle_it	2.7
r_scbond_it	1.714
r_angle_refined_deg	1.447
r_mcangle_it	1.303
r_mcbond_it	0.747
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.222
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.151
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11681
Nucleic Acid Atoms
Solvent Atoms	206
Heterogen Atoms	10

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.