5JCX

Trypanosoma brucei PTR1 in complex with inhibitor NP-29


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, 10 mM DTT; crystallization buffer: 0.1 M sodium citrate pH 5, 2.25 M sodium acetate
Crystal Properties
Matthews coefficientSolvent content
1.9336.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.68α = 90
b = 89.73β = 115.71
c = 82.84γ = 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
11.4341.7794.50.0449.22.2171130212.8
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)
11.431.5194.20.35722.1

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 REPLACEMENTTHROUGHOUT2X9G1.4337.33162483861194.40.146040.144230.17953RANDOM21.037
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]
0.03-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.119
r_sphericity_free32.988
r_dihedral_angle_4_deg17.295
r_sphericity_bonded12.677
r_dihedral_angle_3_deg12.012
r_dihedral_angle_1_deg5.464
r_long_range_B_refined3.631
r_mcangle_it2.665
r_scbond_it2.444
r_rigid_bond_restr2.363
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.119
r_sphericity_free32.988
r_dihedral_angle_4_deg17.295
r_sphericity_bonded12.677
r_dihedral_angle_3_deg12.012
r_dihedral_angle_1_deg5.464
r_long_range_B_refined3.631
r_mcangle_it2.665
r_scbond_it2.444
r_rigid_bond_restr2.363
r_mcbond_it2.194
r_angle_refined_deg1.418
r_chiral_restr0.084
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms7214
Nucleic Acid Atoms
Solvent Atoms664
Heterogen Atoms233

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing