6RX5

Trypanosoma brucei PTR1 (TbPTR1) in complex with inhibitor 1 (NMT-C0003)


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
2.1442.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.86α = 90
b = 90.7β = 115.73
c = 82.95γ = 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
11.4257.6799.80.0530.0620.0310.998113.8187289211.1
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)
11.421.599.40.290.3370.170.9262.23.9

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 REPLACEMENTTHROUGHOUT5JDC1.4257.67178068918999.730.139480.137640.1753RANDOM13.928
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.505
r_sphericity_free25.894
r_dihedral_angle_4_deg17.009
r_dihedral_angle_3_deg12.057
r_sphericity_bonded11.738
r_dihedral_angle_1_deg5.797
r_long_range_B_refined3.256
r_scbond_it1.931
r_rigid_bond_restr1.856
r_mcangle_it1.777
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.505
r_sphericity_free25.894
r_dihedral_angle_4_deg17.009
r_dihedral_angle_3_deg12.057
r_sphericity_bonded11.738
r_dihedral_angle_1_deg5.797
r_long_range_B_refined3.256
r_scbond_it1.931
r_rigid_bond_restr1.856
r_mcangle_it1.777
r_angle_refined_deg1.698
r_mcbond_it1.428
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.009
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7259
Nucleic Acid Atoms
Solvent Atoms904
Heterogen Atoms301

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing