3N9J

Structure of human Glutathione Transferase Pi class in complex with Ethacraplatin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5293100mM MES, pH 5.5, pH 6.0, 28% (w/v) PEG 8000, 20mM CaCl2 10mM DTT, 3mM EACPT, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5251.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.806α = 90
b = 89.994β = 98.24
c = 68.87γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2006-12-05MSINGLE 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
11.8520.2899.80.060.0616.93.7394833948321.98
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)
11.851.9599.60.40.41.93.65695

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 FourierTHROUGHOUT5GSS1.8520.2839483202699.890.180.1780.218RANDOM20.291
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]
1.56-0.68-0.79-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.294
r_dihedral_angle_4_deg14.826
r_dihedral_angle_3_deg12.703
r_dihedral_angle_1_deg5.352
r_scangle_it3.135
r_scbond_it2.107
r_angle_refined_deg1.554
r_mcangle_it1.276
r_mcbond_it0.873
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.294
r_dihedral_angle_4_deg14.826
r_dihedral_angle_3_deg12.703
r_dihedral_angle_1_deg5.352
r_scangle_it3.135
r_scbond_it2.107
r_angle_refined_deg1.554
r_mcangle_it1.276
r_mcbond_it0.873
r_nbtor_refined0.302
r_nbd_refined0.198
r_symmetry_hbond_refined0.163
r_symmetry_vdw_refined0.154
r_chiral_restr0.144
r_xyhbond_nbd_refined0.138
r_metal_ion_refined0.119
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3262
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms67

Software

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