5K6A

Trypanosoma brucei Pteridine reductase 1 (PTR1) in complex with compound 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GN1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION298Protein 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
2.0439.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.72α = 90
b = 89.894β = 115.75
c = 82.684γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2014-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R0.999ELETTRA5.2R

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
11.774.4792.660.0856.72.39566028.864
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)
11.71.74293.50.3221.82.2

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 REPLACEMENTTHROUGHOUT3gn11.774.4795660485992.660.181540.179620.2197RANDOM18.612
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_2_deg35.379
r_dihedral_angle_4_deg17.428
r_dihedral_angle_3_deg13.769
r_dihedral_angle_1_deg7.17
r_long_range_B_refined5.106
r_mcangle_it2.212
r_angle_refined_deg1.883
r_scbond_it1.829
r_mcbond_it1.465
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.379
r_dihedral_angle_4_deg17.428
r_dihedral_angle_3_deg13.769
r_dihedral_angle_1_deg7.17
r_long_range_B_refined5.106
r_mcangle_it2.212
r_angle_refined_deg1.883
r_scbond_it1.829
r_mcbond_it1.465
r_chiral_restr0.12
r_bond_refined_d0.017
r_gen_planes_refined0.01
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7210
Nucleic Acid Atoms
Solvent Atoms773
Heterogen Atoms276

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing