3K96

2.1 Angstrom resolution crystal structure of glycerol-3-phosphate dehydrogenase (gpsA) from Coxiella burnetii

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	Protein solution: 7.6 mg/mL, 0.5M Sodium chloride, 5mM BME, 0.01M Tris-HCl pH 8.3. Screen solution: PEG's II, drop G10, 0.1M Lithium chloride, 0.1M HEPES pH 7.5, 25% w/v PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.272	α = 90
b = 88.452	β = 90
c = 97.289	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	Beryllium lenses	2009-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	30	99.9	0.09	21.02	7.3	44246	44246		-3	33.5

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	2.1	2.14	100		0.628	3.4	7.2	2190

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	PDB entry 1Z82	2.1	29.27	41380	41380	2197	99.9	0.16654	0.16654	0.16422	0.21037	RANDOM	28.017

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]
-1.14			2.76		-1.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.663
r_dihedral_angle_4_deg	11.74
r_dihedral_angle_3_deg	10.015
r_scangle_it	4.706
r_scbond_it	2.891
r_dihedral_angle_1_deg	2.599
r_mcangle_it	1.834
r_angle_refined_deg	1.388
r_mcbond_it	1.023
r_angle_other_deg	0.867

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.663
r_dihedral_angle_4_deg	11.74
r_dihedral_angle_3_deg	10.015
r_scangle_it	4.706
r_scbond_it	2.891
r_dihedral_angle_1_deg	2.599
r_mcangle_it	1.834
r_angle_refined_deg	1.388
r_mcbond_it	1.023
r_angle_other_deg	0.867
r_mcbond_other	0.277
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4970
Nucleic Acid Atoms
Solvent Atoms	481
Heterogen Atoms	34

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.