2PGT

CRYSTAL STRUCTURE OF HUMAN GLUTATHIONE S-TRANSFERASE P1-1[V104] COMPLEXED WITH (9R,10R)-9-(S-GLUTATHIONYL)-10-HYDROXY-9,10-DIHYDROPHENANTHRENE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PGTPDB ENTRY 1PGT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7CRYSTALS WERE GROWN IN HANGING DROPS WHICH INITIALLY CONSISTED OF 5.9 MG/ML PROTEIN IN 0.1 M HEPES BUFFER (PH 7.0) CONTAINING 8.3 MM S-HEXYLGLUTATHIONE AND 1.0 M BUFFERED (PH 7.0) AMMONIUM SULFATE. THE DROPS WERE EQUILIBRATED AT 293 K AGAINST WELL SOLUTION CONTAINING BETWEEN 1.9 - 2.0 M AMMONIUM SULFATE IN 0.1 M HEPES BUFFER (PH 7.0)., vapor diffusion - hanging drop
Crystal Properties
Matthews coefficientSolvent content
2.449

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.18α = 90
b = 90.54β = 98.45
c = 69.37γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATERIGAKU RAXIS IIMIRRORS1996-04-16M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH2R

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
11.92095.50.05912.313.94045623.61
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)
1.91.9377.30.2871.771.45

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONDIFFERENCE FOURIERTHROUGHOUTPDB ENTRY 1PGT1.9634045630838830.18326.04
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_staggered_tor18.2
p_transverse_tor17.9
p_planar_tor6.9
p_scangle_it1.995
p_scbond_it1.298
p_mcangle_it1.225
p_mcbond_it0.726
p_singtor_nbd0.224
p_xyhbond_nbd0.217
p_chiral_restr0.183
RMS Deviations
KeyRefinement Restraint Deviation
p_staggered_tor18.2
p_transverse_tor17.9
p_planar_tor6.9
p_scangle_it1.995
p_scbond_it1.298
p_mcangle_it1.225
p_mcbond_it0.726
p_singtor_nbd0.224
p_xyhbond_nbd0.217
p_chiral_restr0.183
p_multtor_nbd0.176
p_planar_d0.072
p_angle_d0.034
p_plane_restr0.023
p_bond_d0.017
p_angle_deg
p_hb_or_metal_coord
p_xhyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3282
Nucleic Acid Atoms
Solvent Atoms344
Heterogen Atoms100

Software

Software
Software NamePurpose
X-PLORmodel building
GPRLSArefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing