4YQU

Glutathione S-transferase Omega 1 bound to covalent inhibitor C1-31


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EEM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293The GSTO1-C1-31 complex was concentrated to 23.9 mg/mL prior to crystallization. Crystals formed from drops containing equal volumes of complex and well solution (22.5% PEG 3350, 90 mM MES pH 6.5 and 4% tert-butanol).
Crystal Properties
Matthews coefficientSolvent content
2.4649.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.645α = 90
b = 72.588β = 112.69
c = 65.31γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002012-10-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

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
11.945093.40.074163.13674530.08
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)
11.941.9797.50.3432.91926

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1EEM1.9445.2236729185791.580.20490.2030.2403RANDOM34.41
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]
-0.33610.0017-2.24232.5784
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.06
t_other_torsion2.95
t_angle_deg0.94
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion3.06
t_other_torsion2.95
t_angle_deg0.94
t_bond_d0.01
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3743
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms68

Software

Software
Software NamePurpose
BUSTER-TNTrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction