6RX0

Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 3 (NMT-C0013)


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
2.0640.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.854α = 90
b = 90.502β = 115.77
c = 82.951γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-05-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91731DiamondI04-1

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
11.257.6190.50.0450.0540.030.99910.62.628014429.3
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)
11.21.2689.80.350.4350.2540.8672.52.5

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 REPLACEMENTTHROUGHOUT5jdc1.257.612660011406790.410.128850.127580.15245RANDOM12.451
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.212
r_sphericity_free25.225
r_dihedral_angle_4_deg16.297
r_sphericity_bonded12.488
r_dihedral_angle_3_deg11.569
r_dihedral_angle_1_deg5.781
r_long_range_B_refined2.8
r_long_range_B_other2.8
r_scangle_other1.993
r_rigid_bond_restr1.772
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.212
r_sphericity_free25.225
r_dihedral_angle_4_deg16.297
r_sphericity_bonded12.488
r_dihedral_angle_3_deg11.569
r_dihedral_angle_1_deg5.781
r_long_range_B_refined2.8
r_long_range_B_other2.8
r_scangle_other1.993
r_rigid_bond_restr1.772
r_angle_refined_deg1.605
r_scbond_it1.588
r_scbond_other1.588
r_mcangle_other1.425
r_mcangle_it1.423
r_mcbond_it1.184
r_mcbond_other1.183
r_angle_other_deg1.041
r_chiral_restr0.091
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.003
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7186
Nucleic Acid Atoms
Solvent Atoms1064
Heterogen Atoms304

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing