3GUR

Crystal Structure of mu class glutathione S-transferase (GSTM2-2) in complex with glutathione and 6-(7-Nitro-2,1,3-benzoxadiazol-4-ylthio)hexanol (NBDHEX)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HNCPDB ENTRY 1HNC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629816% PEG 8000, 200mM NaCl, 100mM MES , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3748.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.75α = 90
b = 78.016β = 90
c = 219.362γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
12.5109.793.20.08618.324.832108321081142.1
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)
12.52.5983.10.17.01

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1HNC2.529.4330437160692.910.216230.213310.27345RANDOM26.211
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]
-0.74-1.161.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.98
r_dihedral_angle_4_deg19.461
r_dihedral_angle_3_deg16.017
r_dihedral_angle_1_deg7.35
r_scangle_it1.97
r_angle_refined_deg1.454
r_scbond_it1.218
r_mcangle_it0.92
r_mcbond_it0.557
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.98
r_dihedral_angle_4_deg19.461
r_dihedral_angle_3_deg16.017
r_dihedral_angle_1_deg7.35
r_scangle_it1.97
r_angle_refined_deg1.454
r_scbond_it1.218
r_mcangle_it0.92
r_mcbond_it0.557
r_nbtor_refined0.306
r_nbd_refined0.198
r_xyhbond_nbd_refined0.144
r_symmetry_vdw_refined0.136
r_symmetry_hbond_refined0.136
r_chiral_restr0.109
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7181
Nucleic Acid Atoms
Solvent Atoms167
Heterogen Atoms124

Software

Software
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling