5JDI

Trypanosoma brucei PTR1 in complex with cofactor and inhibitor NMT-H024 (compound 2)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP298Protein solution: 6 g/L in 20 mM Tris-HCl pH 7.5, 10 mM DTT; Crystallization buffer: 0.1 M sodium citrate pH 5, 2.25 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
2.4249.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.88α = 90
b = 90.84β = 115.7
c = 82.9γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9184DiamondI03

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
11.3857.799.70.0599.63.12042222
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)
11.381.4599.40.3392.83

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 REPLACEMENTTHROUGHOUT2x9g1.3857.71939081008499.630.11680.1150.15046RANDOM15.672
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]
0.010.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.924
r_sphericity_free32.332
r_dihedral_angle_4_deg18.261
r_sphericity_bonded11.965
r_dihedral_angle_3_deg11.898
r_rigid_bond_restr7.249
r_dihedral_angle_1_deg7.019
r_long_range_B_refined3.851
r_long_range_B_other3.851
r_scangle_other3.445
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.924
r_sphericity_free32.332
r_dihedral_angle_4_deg18.261
r_sphericity_bonded11.965
r_dihedral_angle_3_deg11.898
r_rigid_bond_restr7.249
r_dihedral_angle_1_deg7.019
r_long_range_B_refined3.851
r_long_range_B_other3.851
r_scangle_other3.445
r_scbond_it2.975
r_scbond_other2.975
r_mcangle_it2.542
r_mcangle_other2.542
r_angle_refined_deg2.391
r_mcbond_it2.38
r_mcbond_other2.38
r_angle_other_deg1.192
r_chiral_restr0.167
r_bond_refined_d0.027
r_gen_planes_refined0.014
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 Atoms7212
Nucleic Acid Atoms
Solvent Atoms905
Heterogen Atoms264

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing