4QGR

Crystal structure of a DegT DnrJ EryC1 StrS aminotransferase from Brucella abortus

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	BrabA.17333.a.B1.PS02033 at 20 mg/mL against MCSG-1 screen condition F2 0.2 M ammonium acetate, 0.1 M BisTris HCl pH 6.5, 25% PEG 3350 supplemented with 25% ethylene glycol as cryo-protectant, crystal tracking ID 254589f2, unique puck ID xrf9-6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.69	α = 90
b = 92.06	β = 96.82
c = 86.41	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 315r		2014-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL7-1	1.12709	SSRL	BL7-1

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	1.75	50	99.5	0.072	13.61	3.7	74703	74295		-3	25.269

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	1.75	1.8	99		0.547	2.32

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	3NU7	1.75	50	74272	3688	99.47	0.1574	0.1559	0.1851	RANDOM	24.456

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]
0.02		0.03	-1.38		1.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.425
r_dihedral_angle_4_deg	17.349
r_dihedral_angle_3_deg	11.827
r_dihedral_angle_1_deg	5.716
r_angle_refined_deg	1.461
r_mcangle_it	1.335
r_mcbond_it	0.833
r_mcbond_other	0.824
r_angle_other_deg	0.811
r_chiral_restr	0.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.425
r_dihedral_angle_4_deg	17.349
r_dihedral_angle_3_deg	11.827
r_dihedral_angle_1_deg	5.716
r_angle_refined_deg	1.461
r_mcangle_it	1.335
r_mcbond_it	0.833
r_mcbond_other	0.824
r_angle_other_deg	0.811
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5660
Nucleic Acid Atoms
Solvent Atoms	714
Heterogen Atoms	41

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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.