2WP5

Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00065414)


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
2.550.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.94α = 90
b = 63.3β = 98.09
c = 169.41γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2007-12-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.846.780.50.1310.82.544043222.916
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)
12.82.8779.90.334.372.4

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 2WOI2.846.7114404122031000.1670.16420.2193RANDOM16.067
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]
1.2510.641-0.2-0.871
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.986
r_dihedral_angle_4_deg19.79
r_dihedral_angle_3_deg19.159
r_dihedral_angle_1_deg7.301
r_scangle_it3.149
r_scbond_it1.911
r_angle_refined_deg1.795
r_mcangle_it1.217
r_mcbond_it0.639
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.986
r_dihedral_angle_4_deg19.79
r_dihedral_angle_3_deg19.159
r_dihedral_angle_1_deg7.301
r_scangle_it3.149
r_scbond_it1.911
r_angle_refined_deg1.795
r_mcangle_it1.217
r_mcbond_it0.639
r_nbtor_refined0.319
r_symmetry_vdw_refined0.271
r_symmetry_hbond_refined0.252
r_nbd_refined0.242
r_xyhbond_nbd_refined0.171
r_chiral_restr0.114
r_bond_refined_d0.017
r_metal_ion_refined0.014
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_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 Atoms14782
Nucleic Acid Atoms
Solvent Atoms207
Heterogen Atoms350

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing