5L8C

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-039


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527720% PEG 3350, 0.4 M sodium formate, 0.3 M guanidine, 0.1 M MES
Crystal Properties
Matthews coefficientSolvent content
2.7655.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.6α = 90
b = 115.13β = 108.12
c = 68.63γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2016-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.0157.5699.40.0940.9979.63.455896
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)
12.012.0699.41.2031.33.4

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2.0157.0653212268299.370.197480.195430.23748RANDOM48.762
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]
6.71-1.1-0.85-4.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.528
r_dihedral_angle_3_deg15.815
r_dihedral_angle_4_deg15.351
r_long_range_B_refined8.692
r_long_range_B_other8.689
r_scangle_other6.685
r_dihedral_angle_1_deg5.847
r_mcangle_it5.437
r_mcangle_other5.436
r_scbond_it4.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.528
r_dihedral_angle_3_deg15.815
r_dihedral_angle_4_deg15.351
r_long_range_B_refined8.692
r_long_range_B_other8.689
r_scangle_other6.685
r_dihedral_angle_1_deg5.847
r_mcangle_it5.437
r_mcangle_other5.436
r_scbond_it4.5
r_scbond_other4.492
r_mcbond_it3.692
r_mcbond_other3.692
r_angle_refined_deg1.693
r_angle_other_deg1.3
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.006
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 Atoms5260
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Cootmodel building