8UDE | pdb_00008ude

Crystal Structure of Mu class Glutathione-S-Transferase, TuGSTm06(Tetur05g05220) from Tetranychus urticae


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelSwissModel 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82932 M ammonium sulfate, 0.1 M Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
3.2562.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 135.802α = 90
b = 135.802β = 90
c = 191.998γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-12-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Rpim I (All)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
12.254099.50.0940.0423.95.362541-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.290.5860.2510.7732.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.2539.23362374313599.5230.1990.19670.20370.23570.241663.802
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]
0.3720.1860.372-1.208
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.033
r_dihedral_angle_3_deg13.919
r_dihedral_angle_2_deg11.714
r_lrange_other9.775
r_lrange_it9.761
r_scangle_it9.134
r_scangle_other8.742
r_scbond_it6.785
r_scbond_other6.485
r_mcangle_other6.054
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7267
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms140

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing