3G7Q

Crystal structure of valine-pyruvate aminotransferase AvtA (NP_462565.1) from Salmonella typhimurium LT2 at 1.80 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	NANODROP, 40.0% Ethylene glycol, 0.1M Acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.94	58.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.28	α = 90
b = 92.28	β = 90
c = 227.33	γ = 120

Symmetry
Space Group	P 61 2 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	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2008-11-12	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97874, 0.97828	SSRL	BL11-1

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	1.8	29.285	99.8	0.066	14.25	10.2		53916		-3	28.602

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	1.8	1.86	98.2		0.943	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.8	29.28	53818	2733	99.83	0.17886	0.17797	0.19577	RANDOM	29.685

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]
0.1	0.05		0.1		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.893
r_dihedral_angle_4_deg	16.627
r_dihedral_angle_3_deg	10.367
r_scangle_it	6.383
r_scbond_it	4.478
r_dihedral_angle_1_deg	3.945
r_mcangle_it	2.677
r_mcbond_it	1.806
r_angle_refined_deg	1.589
r_angle_other_deg	1.018
r_mcbond_other	0.424
r_nbd_refined	0.229
r_symmetry_vdw_refined	0.224
r_symmetry_vdw_other	0.202
r_xyhbond_nbd_refined	0.19
r_nbd_other	0.183
r_nbtor_refined	0.18
r_symmetry_hbond_refined	0.176
r_nbtor_other	0.085
r_chiral_restr	0.076
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2976
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing