2GWD | pdb_00002gwd

Crystal structure of plant glutamate cysteine ligase in complex with Mg2+ and L-glutamate

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	18% PEG 3350, 0.2 M magnesium acetate tetrahydrate, 0.1 M tricine, 0.05 M L-glutamate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.81	α = 90
b = 54.81	β = 90
c = 518.04	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	Large Area Detector		2004-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.9782	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.09	47.46	94.8	0.062	27.2	11	27931	27931	-3	-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.22	70.5		0.13	5.7	2.1	3283

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	2GWC monomer	2.09	47.46	-3	27818	26427	1391	100	0.178	0.178	0.17532	0.19	0.2267	0.23	RANDOM	20.333

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]
0.12	0.06		0.12		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.32
r_dihedral_angle_4_deg	17.123
r_dihedral_angle_3_deg	13.95
r_dihedral_angle_1_deg	6.319
r_scangle_it	2.323
r_scbond_it	1.604
r_angle_refined_deg	1.314
r_mcangle_it	0.821
r_angle_other_deg	0.812
r_mcbond_it	0.722
r_nbd_refined	0.21
r_symmetry_vdw_other	0.209
r_nbd_other	0.185
r_symmetry_vdw_refined	0.183
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.142
r_mcbond_other	0.136
r_nbtor_other	0.083
r_symmetry_hbond_refined	0.075
r_chiral_restr	0.073
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	3495
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PHASER	phasing