6JI6

Crystal structure of glutathione S-transferase complexed and modified with glutathione


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UA5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M Bis-Tris, 0.4M Ammonium acetate, 26% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.5151.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.708α = 90
b = 93.708β = 90
c = 57.609γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS3 S 2M2018-02-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.55097.20.1880.1920.039116.222.34021722.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.551000.7080.7420.2150.8582.611.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1UA51.55037812199996.040.192420.19080.2237RANDOM16.48
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]
0.060.06-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.383
r_dihedral_angle_4_deg15.122
r_dihedral_angle_3_deg11.242
r_long_range_B_refined5.531
r_long_range_B_other5.531
r_dihedral_angle_1_deg5.394
r_scangle_other2.268
r_mcangle_it1.523
r_mcangle_other1.523
r_angle_refined_deg1.467
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.383
r_dihedral_angle_4_deg15.122
r_dihedral_angle_3_deg11.242
r_long_range_B_refined5.531
r_long_range_B_other5.531
r_dihedral_angle_1_deg5.394
r_scangle_other2.268
r_mcangle_it1.523
r_mcangle_other1.523
r_angle_refined_deg1.467
r_scbond_it1.414
r_scbond_other1.413
r_mcbond_it0.918
r_mcbond_other0.912
r_angle_other_deg0.844
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1770
Nucleic Acid Atoms
Solvent Atoms375
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing