2YHI

Trypanosoma brucei PTR1 in complex with inhibitor WH16


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X9GPDB ENTRY 2X9G

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5RESERVOIR CONDITIONS: 100 MM SODIUM CITRATE PH 5, 1.8 M SODIUM ACETATE.
Crystal Properties
Matthews coefficientSolvent content
2.141.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.28α = 90
b = 90.74β = 115.66
c = 84.29γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDMIRRORS2009-10-04MSINGLE 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
11.831.4194.50.0715.85.28790420.86
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)
11.81.988.40.562.74.5

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 2X9G1.831.4183470441394.190.180090.178640.20716RANDOM19.61
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]
-0.83-0.362.12-1.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.415
r_dihedral_angle_4_deg15.477
r_dihedral_angle_3_deg13.71
r_dihedral_angle_1_deg5.317
r_scangle_it2.095
r_scbond_it1.3
r_angle_refined_deg1.17
r_mcangle_it0.874
r_mcbond_it0.455
r_chiral_restr0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.415
r_dihedral_angle_4_deg15.477
r_dihedral_angle_3_deg13.71
r_dihedral_angle_1_deg5.317
r_scangle_it2.095
r_scbond_it1.3
r_angle_refined_deg1.17
r_mcangle_it0.874
r_mcbond_it0.455
r_chiral_restr0.069
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms7418
Nucleic Acid Atoms
Solvent Atoms536
Heterogen Atoms268

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing