5SA3

PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z2856434874


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8298MPD 22%, PEG 3350 14%, imidazole 40 mM pH 8
Crystal Properties
Matthews coefficientSolvent content
2.2946.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.57α = 90
b = 108.62β = 90
c = 112.04γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-01-13SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91266DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.7480.5799.60.0850.0920.0350.99811.36.7100864
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.741.79992.2162.3920.8940.32477344

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT6RB51.7477.9995896490099.460.1870.18550.2172RANDOM33.662
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]
0.35-0.680.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.942
r_dihedral_angle_4_deg18.26
r_dihedral_angle_3_deg14.948
r_dihedral_angle_1_deg6.998
r_mcangle_it3.208
r_mcbond_it2.478
r_mcbond_other2.474
r_angle_refined_deg1.544
r_angle_other_deg1.379
r_chiral_restr0.077
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.942
r_dihedral_angle_4_deg18.26
r_dihedral_angle_3_deg14.948
r_dihedral_angle_1_deg6.998
r_mcangle_it3.208
r_mcbond_it2.478
r_mcbond_other2.474
r_angle_refined_deg1.544
r_angle_other_deg1.379
r_chiral_restr0.077
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7360
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms170

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing