2WPE

Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00073359)


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
2.4549.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.64α = 90
b = 63.29β = 98.2
c = 169.16γ = 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
12.14695.30.1215.94.4123374231.6
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)
12.12.1587.70.463.24.4

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 2WOI2.145.97912337461691000.1710.1680.23RANDOM27.723
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]
1.3450.38-0.156-1.081
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.647
r_dihedral_angle_4_deg18.402
r_dihedral_angle_3_deg16.98
r_dihedral_angle_1_deg6.861
r_scangle_it4.847
r_scbond_it3.179
r_angle_refined_deg1.946
r_mcangle_it1.839
r_mcbond_it1.096
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.647
r_dihedral_angle_4_deg18.402
r_dihedral_angle_3_deg16.98
r_dihedral_angle_1_deg6.861
r_scangle_it4.847
r_scbond_it3.179
r_angle_refined_deg1.946
r_mcangle_it1.839
r_mcbond_it1.096
r_nbtor_refined0.314
r_symmetry_vdw_refined0.262
r_nbd_refined0.217
r_symmetry_hbond_refined0.184
r_xyhbond_nbd_refined0.158
r_chiral_restr0.139
r_metal_ion_refined0.132
r_bond_refined_d0.024
r_gen_planes_refined0.011
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_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 Atoms14796
Nucleic Acid Atoms
Solvent Atoms1216
Heterogen Atoms362

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing