5V0S | pdb_00005v0s

Crystal structure of the ACT domain of prephenate dehydrogenase tyrA from Bacillus anthracis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 500 mM NaCl, 5% Glycerol, and 10 mM BME were mixed with 0.2 ul of the MCSG Suite I condition #31 (0.1 M Tris pH=8.5, 0.2 M Calcium chloride, 25% w/v PEG 4000) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.07	α = 90
b = 48.07	β = 90
c = 233.395	γ = 120

Symmetry
Space Group	P 65 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 225 mm CCD	Beryllium Lenses	2014-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	50	96.9	0.053	0.053	0.057	0.018	9.8	7.4		11294		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.03	88.1		0.619	0.619	0.653	0.195	0.844	1.7	7.5

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.01	41.63	10640	565	96.68	0.1737	0.1708	0.18	0.2323	0.25	RANDOM	53.642

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	0.5		1		-3.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.549
r_dihedral_angle_4_deg	18.11
r_dihedral_angle_3_deg	15.554
r_dihedral_angle_1_deg	5.263
r_angle_refined_deg	1.501
r_angle_other_deg	0.876
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.549
r_dihedral_angle_4_deg	18.11
r_dihedral_angle_3_deg	15.554
r_dihedral_angle_1_deg	5.263
r_angle_refined_deg	1.501
r_angle_other_deg	0.876
r_chiral_restr	0.088
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1060
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	7

Software

Software
Software Name	Purpose
MD2	data collection
HKL-3000	data reduction
HKL-2000	data scaling
SHELX	phasing
MLPHARE	phasing
DM	phasing
HKL-3000	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	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.