5JDC

Trypanosoma brucei PTR1 in complex with inhibitor NP-13 (Hesperetin)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Protein solution: 8 g/L in 20 mM Tris-HCl pH 7.5, 10mM DTT; Crystallization buffer: 0.1 M Sodium Citrate pH 5, 2.25 M Sodium Acetate
Crystal Properties
Matthews coefficientSolvent content
2.1943.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.84α = 90
b = 90.04β = 115.78
c = 82.94γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.7853.6898.70.0896.1392591221.2
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)
11.781.8898.50.371.92.9

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 REPLACEMENTTHROUGHOUT2X9G1.7853.6889348461599.080.209490.207890.24057RANDOM21.656
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.933
r_dihedral_angle_4_deg15.503
r_dihedral_angle_3_deg13.925
r_dihedral_angle_1_deg7.63
r_long_range_B_refined5.557
r_long_range_B_other5.557
r_scangle_other4.177
r_mcangle_it2.777
r_mcangle_other2.777
r_scbond_it2.709
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.933
r_dihedral_angle_4_deg15.503
r_dihedral_angle_3_deg13.925
r_dihedral_angle_1_deg7.63
r_long_range_B_refined5.557
r_long_range_B_other5.557
r_scangle_other4.177
r_mcangle_it2.777
r_mcangle_other2.777
r_scbond_it2.709
r_scbond_other2.706
r_angle_refined_deg1.984
r_mcbond_it1.864
r_mcbond_other1.862
r_angle_other_deg1.077
r_chiral_restr0.109
r_bond_refined_d0.018
r_gen_planes_refined0.009
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7263
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms294

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing