3DD3

Crystal Structure of the Glutathione Transferase Pi enzyme in complex with the bifunctional inhibitor, Etharapta


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5298100mM MES buffer pH 5.5 or 6.0, 22%(w/v) PEG 8000, 20mM CaCl2, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5150.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.69α = 90
b = 89.54β = 97.81
c = 68.99γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDmirrors2007-08-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.77APS23-ID-B

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
12.2568.3699.50.10.14.33.6219832186536.96
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)
12.252.3796.60.560.56133071

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 REPLACEMENTTHROUGHOUT5GSS2.2568.362186220718114499.450.240.20.20.26RANDOM43.88
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]
6.61-0.66-2.9-3.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.697
r_dihedral_angle_4_deg16.664
r_dihedral_angle_3_deg15.919
r_dihedral_angle_1_deg6.052
r_scangle_it3.479
r_scbond_it2.28
r_angle_refined_deg1.606
r_mcangle_it1.542
r_mcbond_it0.927
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.697
r_dihedral_angle_4_deg16.664
r_dihedral_angle_3_deg15.919
r_dihedral_angle_1_deg6.052
r_scangle_it3.479
r_scbond_it2.28
r_angle_refined_deg1.606
r_mcangle_it1.542
r_mcbond_it0.927
r_nbtor_refined0.311
r_nbd_refined0.22
r_symmetry_vdw_refined0.193
r_xyhbond_nbd_refined0.173
r_symmetry_hbond_refined0.148
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3277
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms71

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
MOSFLMdata reduction
REFMACphasing