3NZT | pdb_00003nzt

2.0 Angstrom Crystal structure of Glutamate--Cysteine Ligase (gshA) ftom Francisella tularensis in Complex with AMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D32

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	295	protein: 7.3 mg/mL, 0.5M Sodium chloride, Tris-HCl (pH 8.3), 1mM AMPPNP, 1mM Magnesium chloride, screen: ClassicsII, drop A2, 0.1M Sodium acetate (pH 4.5), 2M Ammonium sulphate, Cryo: 1.8M Ammonium sulphate, 25% Sucrose, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.96	58.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.849	α = 90
b = 89.849	β = 90
c = 151.468	γ = 120

Symmetry
Space Group	P 65

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	2010-03-08	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)	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	30	100	0.063	25.2	5.7	46618	46618		-3	30.3

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)
	2	2.03	100		0.468	3.9	5.7	2296

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2D32	2	29.41	44206	44206	2351	99.93	0.16548	0.16548	0.1639	0.17	0.19598	0.2	RANDOM	29.23

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]
0.84	0.42		0.84		-1.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.071
r_dihedral_angle_4_deg	17.779
r_dihedral_angle_3_deg	10.48
r_scangle_it	4.324
r_dihedral_angle_1_deg	3.149
r_scbond_it	2.674
r_mcangle_it	1.564
r_angle_refined_deg	1.372
r_mcbond_it	0.852
r_angle_other_deg	0.848

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.071
r_dihedral_angle_4_deg	17.779
r_dihedral_angle_3_deg	10.48
r_scangle_it	4.324
r_dihedral_angle_1_deg	3.149
r_scbond_it	2.674
r_mcangle_it	1.564
r_angle_refined_deg	1.372
r_mcbond_it	0.852
r_angle_other_deg	0.848
r_mcbond_other	0.244
r_chiral_restr	0.09
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	3977
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	78

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	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.