3HKR

Crystal Structure of Glutathione Transferase Pi Y108V Mutant


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298267mM Calcium Acetate, 20% PEG8000, 100mM MES, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5651.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.1α = 90
b = 90.3β = 98.2
c = 68.9γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2008-09-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.96Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.7410098.30.0622.377.347590-324.854
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.741.8489.80.34.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB ENTRY 5GSS1.842.1143129224899.720.170.170.170.21RANDOM19.247
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]
0.18-0.05-0.07-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.673
r_dihedral_angle_4_deg15.818
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg5.17
r_scangle_it3.04
r_scbond_it1.998
r_angle_refined_deg1.32
r_mcangle_it1.235
r_mcbond_it0.848
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.673
r_dihedral_angle_4_deg15.818
r_dihedral_angle_3_deg12.956
r_dihedral_angle_1_deg5.17
r_scangle_it3.04
r_scbond_it1.998
r_angle_refined_deg1.32
r_mcangle_it1.235
r_mcbond_it0.848
r_nbtor_refined0.307
r_symmetry_vdw_refined0.206
r_nbd_refined0.198
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.131
r_metal_ion_refined0.099
r_chiral_restr0.088
r_bond_refined_d0.013
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3260
Nucleic Acid Atoms
Solvent Atoms490
Heterogen Atoms41

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing