6FDW

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-356


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I15 

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
2.6553.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.69α = 90
b = 119.26β = 108.38
c = 67.97γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6MCRL2017-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

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
11.9633.9199.50.0460.0550.030.99913.63.460184
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)
11.962.0199.80.9371.110.5890.6041.43.4

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 REPLACEMENTTHROUGHOUT4I151.9633.9157112306899.450.192210.189810.23697RANDOM52.319
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]
3.640.07-0.56-2.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.987
r_dihedral_angle_3_deg16.81
r_dihedral_angle_4_deg16.444
r_long_range_B_refined9.105
r_long_range_B_other9.105
r_scangle_other7.118
r_mcangle_other6.399
r_mcangle_it6.398
r_dihedral_angle_1_deg6.276
r_scbond_it5.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.987
r_dihedral_angle_3_deg16.81
r_dihedral_angle_4_deg16.444
r_long_range_B_refined9.105
r_long_range_B_other9.105
r_scangle_other7.118
r_mcangle_other6.399
r_mcangle_it6.398
r_dihedral_angle_1_deg6.276
r_scbond_it5.002
r_scbond_other5.001
r_mcbond_it4.658
r_mcbond_other4.655
r_angle_refined_deg1.796
r_angle_other_deg1.078
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.002
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 Atoms5252
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing