2WPF

Trypanosoma brucei trypanothione reductase in complex with 3,4- dihydroquinazoline inhibitor (DDD00085762)


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, 50MM NABR EQUILIBRATED AGAINST 24% MPD, 10% PEG 3350, 40MM IMIDAZOLE PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.3848.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.82α = 90
b = 62.76β = 98.13
c = 167.44γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMIRRORS2008-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
11.919.999.10.119.73.9160960226.7
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)
11.91.9595.10.3333.6

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 2WOI1.919.88816096080481000.1880.18490.2467RANDOM24.316
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]
0.7890.452-0.299-0.362
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg19.829
r_dihedral_angle_3_deg17.075
r_dihedral_angle_1_deg6.804
r_scangle_it4.583
r_scbond_it3.035
r_angle_refined_deg1.963
r_mcangle_it1.784
r_mcbond_it1.079
r_nbtor_refined0.324
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.892
r_dihedral_angle_4_deg19.829
r_dihedral_angle_3_deg17.075
r_dihedral_angle_1_deg6.804
r_scangle_it4.583
r_scbond_it3.035
r_angle_refined_deg1.963
r_mcangle_it1.784
r_mcbond_it1.079
r_nbtor_refined0.324
r_symmetry_vdw_refined0.246
r_nbd_refined0.223
r_symmetry_hbond_refined0.202
r_xyhbond_nbd_refined0.164
r_chiral_restr0.132
r_bond_refined_d0.022
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_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 Atoms1293
Heterogen Atoms322

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing