3IE3

Structural basis for the binding of the anti-cancer compound 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX) to human glutathione S-transferases


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GSSPDB ENTRY 6GSS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62771.8M AMMONIUM SULFATE, 100MM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5652.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.869α = 90
b = 89.535β = 98.04
c = 68.916γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4rmirrors2009-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
11.829.2199.10.0580.05817.4442435424351116.5
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)
11.81.86990.1788.05

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 6GSS1.829.2124243540294213298.490.180420.180420.178870.20938RANDOM14.588
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]
1.33-0.12-1.24-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.161
r_dihedral_angle_4_deg15.726
r_dihedral_angle_3_deg10.959
r_dihedral_angle_1_deg4.538
r_angle_refined_deg1.373
r_scangle_it1.116
r_scbond_it0.726
r_mcangle_it0.517
r_mcbond_it0.317
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.161
r_dihedral_angle_4_deg15.726
r_dihedral_angle_3_deg10.959
r_dihedral_angle_1_deg4.538
r_angle_refined_deg1.373
r_scangle_it1.116
r_scbond_it0.726
r_mcangle_it0.517
r_mcbond_it0.317
r_nbtor_refined0.299
r_nbd_refined0.177
r_chiral_restr0.153
r_symmetry_vdw_refined0.104
r_symmetry_hbond_refined0.093
r_xyhbond_nbd_refined0.085
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3263
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms104

Software

Software
Software NamePurpose
ADSCdata collection
FFTmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
FFTphasing