5ZWP

Crystal structure of the delta-class glutathione transferase from Musca domestica


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.62930.2 M sodium citrate, pH 5.6, 1.8 M ammonium sulfate, 0.1 M tartrate
Crystal Properties
Matthews coefficientSolvent content
2.4249.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.26α = 90
b = 90.909β = 107.56
c = 51.418γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2702007-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0000Photon FactoryBL-17A

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
11.449.0395.90.0458.21.984246
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)
11.41.4895.90.1155.91.9

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 REPLACEMENTTHROUGHOUT1JLV1.449.0380001421795.490.157730.156760.17605RANDOM10.854
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]
-0.5-0.051.11-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.238
r_dihedral_angle_4_deg20.812
r_dihedral_angle_3_deg12.581
r_dihedral_angle_1_deg5.497
r_long_range_B_refined3.479
r_long_range_B_other3.479
r_angle_other_deg2.162
r_scangle_other2.131
r_angle_refined_deg1.912
r_scbond_it1.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.238
r_dihedral_angle_4_deg20.812
r_dihedral_angle_3_deg12.581
r_dihedral_angle_1_deg5.497
r_long_range_B_refined3.479
r_long_range_B_other3.479
r_angle_other_deg2.162
r_scangle_other2.131
r_angle_refined_deg1.912
r_scbond_it1.42
r_scbond_other1.415
r_mcangle_it1.101
r_mcangle_other1.101
r_mcbond_it0.712
r_mcbond_other0.712
r_chiral_restr0.106
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3336
Nucleic Acid Atoms
Solvent Atoms486
Heterogen Atoms73

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing