6TBX

Trypanosoma brucei PTR1 (TbPTR1) in complex with a tricyclic-based inhibitor


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5JDC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52942-2.5M sodium acetate, 0.1M sodium citrate, pH 5
Crystal Properties
Matthews coefficientSolvent content
2.141.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.677α = 90
b = 90.779β = 115.65
c = 82.81γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97949DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.345.3996.20.0690.0940.0530.9898.3323420911.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.31.3794.10.4470.640.370.8032.42.8

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 REPLACEMENTTHROUGHOUT5JDC1.341.832223931176796.030.12770.1260.1594RANDOM17.12
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]
-0.03-0.02-0.070.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.042
r_dihedral_angle_4_deg18.427
r_dihedral_angle_3_deg12.029
r_rigid_bond_restr6.793
r_dihedral_angle_1_deg6.242
r_angle_refined_deg1.842
r_angle_other_deg1.663
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.042
r_dihedral_angle_4_deg18.427
r_dihedral_angle_3_deg12.029
r_rigid_bond_restr6.793
r_dihedral_angle_1_deg6.242
r_angle_refined_deg1.842
r_angle_other_deg1.663
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7230
Nucleic Acid Atoms
Solvent Atoms749
Heterogen Atoms270

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing