8PF3

Crystal structure of Trypanosoma brucei trypanothione reductase in complex with 1-(3,4-dichlorobenzyl)-4-(((5-((4-fluorophenethyl)carbamoyl)furan-2-yl)methyl)(4-fluorophenyl)carbamoyl)-1-(3-phenylpropyl)piperazin-1-ium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WOI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29313-15% PEG3350, 22-24% MPD, 40 mM imidazole pH 7.5, 50 mM NaBr
Crystal Properties
Matthews coefficientSolvent content
2.5351.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.703α = 90
b = 63.742β = 97.75
c = 170.096γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-03-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 11.2C1ELETTRA11.2C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.15168.5499.70.99610.376117489
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.280.7412.25

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.15168.54111276580499.620.18130.179020.22408RANDOM42.179
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]
1.520.87-0.72-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.457
r_dihedral_angle_4_deg18.106
r_dihedral_angle_3_deg16.135
r_long_range_B_other8.598
r_long_range_B_refined8.592
r_dihedral_angle_1_deg7.019
r_scangle_other6.011
r_mcangle_other4.412
r_mcangle_it4.411
r_scbond_it3.893
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.457
r_dihedral_angle_4_deg18.106
r_dihedral_angle_3_deg16.135
r_long_range_B_other8.598
r_long_range_B_refined8.592
r_dihedral_angle_1_deg7.019
r_scangle_other6.011
r_mcangle_other4.412
r_mcangle_it4.411
r_scbond_it3.893
r_scbond_other3.892
r_mcbond_it3.068
r_mcbond_other3.065
r_angle_refined_deg1.54
r_angle_other_deg1.27
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.002
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 Atoms14846
Nucleic Acid Atoms
Solvent Atoms595
Heterogen Atoms453

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing