3IG5 | pdb_00003ig5

Saccharomyces cerevisiae glutamate cysteine ligase in complex with Mg2+ and L-glutamate

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	291	12% PEG 400, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.444	α = 90
b = 117.444	β = 90
c = 165.363	γ = 90

Symmetry
Space Group	P 43 21 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	ADSC QUANTUM 315		2008-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9	APS	14-BM-C

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	2.1	50	97.5	0.069	20.9	4.5		66287

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	2.1	2.18	96.1		0.578	1.8	3.6

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 (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	2.1	31.91	54225	2000	100	0.1835	0.1835	0.18217	0.1827	0.21894	0.2214	RANDOM	37.969

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]
0.13			0.13		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.854
r_dihedral_angle_4_deg	17.872
r_dihedral_angle_3_deg	15.013
r_dihedral_angle_1_deg	6.369
r_scangle_it	3.725
r_scbond_it	2.611
r_mcangle_it	1.731
r_angle_refined_deg	1.683
r_mcbond_it	1.028
r_nbtor_refined	0.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.854
r_dihedral_angle_4_deg	17.872
r_dihedral_angle_3_deg	15.013
r_dihedral_angle_1_deg	6.369
r_scangle_it	3.725
r_scbond_it	2.611
r_mcangle_it	1.731
r_angle_refined_deg	1.683
r_mcbond_it	1.028
r_nbtor_refined	0.318
r_symmetry_vdw_refined	0.272
r_nbd_refined	0.215
r_symmetry_hbond_refined	0.184
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.117
r_metal_ion_refined	0.078
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5477
Nucleic Acid Atoms
Solvent Atoms	328
Heterogen Atoms	51

Software

Software
Software Name	Purpose
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

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.