3HJO

Crystal Structure of Glutathione Transferase Pi Y108V Mutant in Complex with the Glutathione Conjugate of Ethacrynic Acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5GSSPDB ENTRY 5GSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.4298133mM Calcium Acetate, 18% PEG8000, 100mM MES, pH5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5151.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.384α = 90
b = 89.375β = 90.07
c = 69.19γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++AXCO2008-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9537.5487.20.080.088.565.62913516.32
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.952.0642.20.380.381.93.52026

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 REPLACEMENTTHROUGHOUTPDB ENTRY 5GSS1.9537.5329133150787.10.160.150.21RANDOM14.39
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]
1.660.01-0.9-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.859
r_dihedral_angle_4_deg15.534
r_dihedral_angle_3_deg12.881
r_dihedral_angle_1_deg5.615
r_scangle_it2.789
r_scbond_it1.903
r_angle_refined_deg1.356
r_mcangle_it1.176
r_mcbond_it0.72
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.859
r_dihedral_angle_4_deg15.534
r_dihedral_angle_3_deg12.881
r_dihedral_angle_1_deg5.615
r_scangle_it2.789
r_scbond_it1.903
r_angle_refined_deg1.356
r_mcangle_it1.176
r_mcbond_it0.72
r_nbtor_refined0.3
r_nbd_refined0.193
r_symmetry_vdw_refined0.15
r_xyhbond_nbd_refined0.139
r_symmetry_hbond_refined0.131
r_metal_ion_refined0.092
r_chiral_restr0.091
r_symmetry_metal_ion_refined0.069
r_bond_refined_d0.014
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3264
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms92

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
PHASERphasing