5S9X

PanDDA analysis group deposition -- Crystal Structure of Trypanosoma brucei Trypanothione reductase in complex with Z1899842917


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
2.2946.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.98α = 90
b = 109.24β = 90
c = 112.13γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2021-01-12SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9126DiamondI04-1

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
11.8478.251000.0990.1080.0420.99810.86.785835
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)
11.841.891002.5522.7631.0540.2976.86279

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 SYNTHESISTHROUGHOUT6RB51.8478.2581508424099.920.19670.19460.2381RANDOM39.025
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]
-0.621.35-0.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.892
r_dihedral_angle_3_deg15.461
r_dihedral_angle_4_deg14.263
r_dihedral_angle_1_deg7.036
r_mcangle_it3.803
r_mcbond_other2.825
r_mcbond_it2.822
r_angle_refined_deg1.483
r_angle_other_deg1.305
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.892
r_dihedral_angle_3_deg15.461
r_dihedral_angle_4_deg14.263
r_dihedral_angle_1_deg7.036
r_mcangle_it3.803
r_mcbond_other2.825
r_mcbond_it2.822
r_angle_refined_deg1.483
r_angle_other_deg1.305
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7360
Nucleic Acid Atoms
Solvent Atoms525
Heterogen Atoms186

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing