8RHV

Crystal Structure of Trypanosoma brucei PTR1 in complex with the cofactor and inhibitor P30


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6TBX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52971.6-2.5 M sodium acetate and 0.1 M sodium citrate, pH 5
Crystal Properties
Matthews coefficientSolvent content
1.9236.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.523α = 90
b = 89.451β = 115.26
c = 82.632γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2023-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.95374DiamondI04

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
11.789.4599.30.0340.0420.024118.25.9106873227.4
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)
11.71.7398.50.6960.8510.4830.80825.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.774.73101395544599.190.183610.181570.2212RANDOM33.023
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.883
r_dihedral_angle_1_deg6.419
r_long_range_B_refined6.075
r_dihedral_angle_2_deg5.002
r_mcangle_it4.086
r_scbond_it3.587
r_mcbond_it3.065
r_angle_refined_deg1.873
r_chiral_restr0.136
r_gen_planes_refined0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg12.883
r_dihedral_angle_1_deg6.419
r_long_range_B_refined6.075
r_dihedral_angle_2_deg5.002
r_mcangle_it4.086
r_scbond_it3.587
r_mcbond_it3.065
r_angle_refined_deg1.873
r_chiral_restr0.136
r_gen_planes_refined0.01
r_bond_refined_d0.009
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7334
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms258

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing