2WP6

Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00071494)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1815MG/ML PROTEIN IN 25MM HEPES PH 7.5 AND 50MM NABR EQUILIBRATED AGAINST 24% MPD, 10% PEG3350 AND 40MM IMIDAZOLE PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.5451.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.65α = 90
b = 63.21β = 97.82
c = 170.5γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2008-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
12.546.896.70.149.44.374819231.033
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)
12.52.5691.40.433.154.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2WOI2.546.7737481937411000.1670.1630.2361RANDOM22.873
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]
0.7780.2420.578-1.291
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.938
r_dihedral_angle_4_deg19.096
r_dihedral_angle_3_deg17.65
r_dihedral_angle_1_deg6.511
r_scangle_it3.848
r_scbond_it2.371
r_angle_refined_deg1.682
r_mcangle_it1.445
r_mcbond_it0.762
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.938
r_dihedral_angle_4_deg19.096
r_dihedral_angle_3_deg17.65
r_dihedral_angle_1_deg6.511
r_scangle_it3.848
r_scbond_it2.371
r_angle_refined_deg1.682
r_mcangle_it1.445
r_mcbond_it0.762
r_nbtor_refined0.313
r_symmetry_vdw_refined0.249
r_nbd_refined0.216
r_xyhbond_nbd_refined0.158
r_symmetry_hbond_refined0.15
r_chiral_restr0.11
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14837
Nucleic Acid Atoms
Solvent Atoms915
Heterogen Atoms317

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing