6HOW

Trypanosoma brucei PTR1 in complex with the triazine inhibitor 2a (F219).


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP52942-2.5 M sodium acetate, 0.1 M sodium citrate, pH5
Crystal Properties
Matthews coefficientSolvent content
2.1141.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.674α = 90
b = 91.042β = 115.59
c = 83.001γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2016-07-09MSINGLE 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
11.9257.821000.0630.0740.0390.99810.73.676465227
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)
11.922.021000.4620.5450.2860.8892.73.6

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 REPLACEMENTTHROUGHOUT5JDC1.9254.272697374099.950.171760.169910.20853RANDOM31.15
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.88
r_dihedral_angle_4_deg18.963
r_dihedral_angle_3_deg14.993
r_long_range_B_refined7.11
r_dihedral_angle_1_deg6.749
r_mcangle_it4.607
r_scbond_it4.327
r_mcbond_it3.421
r_angle_refined_deg2.144
r_chiral_restr0.137
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.88
r_dihedral_angle_4_deg18.963
r_dihedral_angle_3_deg14.993
r_long_range_B_refined7.11
r_dihedral_angle_1_deg6.749
r_mcangle_it4.607
r_scbond_it4.327
r_mcbond_it3.421
r_angle_refined_deg2.144
r_chiral_restr0.137
r_bond_refined_d0.013
r_gen_planes_refined0.012
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_it
r_scangle_other
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 Atoms7110
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms263

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing