2GWD

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GWC2GWC monomer

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829818% 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 coefficientSolvent content
2.244.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.81α = 90
b = 54.81β = 90
c = 518.04γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDLarge Area Detector2004-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.9782SLSX06SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.0947.4694.80.06227.2112793127931-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.092.2270.50.135.72.13283

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GWC monomer2.0947.46-3278182642713911000.1780.1780.175320.2267RANDOM20.333
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]
0.120.060.12-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.32
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg13.95
r_dihedral_angle_1_deg6.319
r_scangle_it2.323
r_scbond_it1.604
r_angle_refined_deg1.314
r_mcangle_it0.821
r_angle_other_deg0.812
r_mcbond_it0.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.32
r_dihedral_angle_4_deg17.123
r_dihedral_angle_3_deg13.95
r_dihedral_angle_1_deg6.319
r_scangle_it2.323
r_scbond_it1.604
r_angle_refined_deg1.314
r_mcangle_it0.821
r_angle_other_deg0.812
r_mcbond_it0.722
r_nbd_refined0.21
r_symmetry_vdw_other0.209
r_nbd_other0.185
r_symmetry_vdw_refined0.183
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.142
r_mcbond_other0.136
r_nbtor_other0.083
r_symmetry_hbond_refined0.075
r_chiral_restr0.073
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3495
Nucleic Acid Atoms
Solvent Atoms245
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing