3KM6

Crystal Structure of the Human GST Pi C47S/Y108V Double Mutant in Complex with the Ethacrynic Acid-Glutathione Conjugate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HJOpdb ID 3HJO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62984mg/ml, 267mM calcium acetate, 100mM MES pH 6.0, 20% (w/v) PEG 8000 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5351.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.876α = 90
b = 89.242β = 89.89
c = 69.206γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-08-01MSINGLE 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
12.144.6398.20.1190.11918.47.326463
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)
12.12.2187.50.3750.3751.86.53412

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 DIFFRACTIONDifference FourierTHROUGHOUTpdb ID 3HJO2.144.6326463131898.170.1550.1530.206RANDOM13.925
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]
1.130.01-0.74-0.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.607
r_dihedral_angle_4_deg17.553
r_dihedral_angle_3_deg12.175
r_dihedral_angle_1_deg5.581
r_scangle_it2.555
r_scbond_it1.721
r_angle_refined_deg1.278
r_mcangle_it1.026
r_mcbond_it0.657
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.607
r_dihedral_angle_4_deg17.553
r_dihedral_angle_3_deg12.175
r_dihedral_angle_1_deg5.581
r_scangle_it2.555
r_scbond_it1.721
r_angle_refined_deg1.278
r_mcangle_it1.026
r_mcbond_it0.657
r_nbtor_refined0.3
r_nbd_refined0.192
r_symmetry_vdw_refined0.158
r_symmetry_hbond_refined0.153
r_xyhbond_nbd_refined0.144
r_symmetry_metal_ion_refined0.115
r_chiral_restr0.083
r_metal_ion_refined0.074
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3259
Nucleic Acid Atoms
Solvent Atoms477
Heterogen Atoms84

Software

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