3KAK

Structure of homoglutathione synthetase from Glycine max in open conformation with gamma-glutamyl-cysteine bound.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherhomoglutathione synthetase apoenzyme

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP727720% PEG3000, 0.1 M 3-(N-morpholino)-2-hydroxypropanesulfonic acid (MOPSO), pH 7, 0.2 M MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0941.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.88α = 90
b = 80.95β = 95.96
c = 89.12γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2007-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-10.979SSRLBL9-1

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
12.119.896.50.10811.43.6529145104329.3
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)
2.12.1692.30.4672.43.87984

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUThomoglutathione synthetase apoenzyme2.1119.8529145005726351000.210640.210640.206540.28797RANDOM29.3
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]
-0.02-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.958
r_dihedral_angle_4_deg23.871
r_dihedral_angle_3_deg21.49
r_dihedral_angle_1_deg10.744
r_scangle_it4.965
r_scbond_it3.453
r_angle_refined_deg2.548
r_mcangle_it2.241
r_mcbond_it1.41
r_symmetry_vdw_refined0.333
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.958
r_dihedral_angle_4_deg23.871
r_dihedral_angle_3_deg21.49
r_dihedral_angle_1_deg10.744
r_scangle_it4.965
r_scbond_it3.453
r_angle_refined_deg2.548
r_mcangle_it2.241
r_mcbond_it1.41
r_symmetry_vdw_refined0.333
r_nbtor_refined0.322
r_nbd_refined0.281
r_symmetry_hbond_refined0.261
r_xyhbond_nbd_refined0.224
r_chiral_restr0.193
r_bond_refined_d0.028
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6993
Nucleic Acid Atoms
Solvent Atoms281
Heterogen Atoms48

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling