6FE3 | pdb_00006fe3

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1439


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house model

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
2.6553.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 115.53α = 90
b = 114.82β = 108.25
c = 68.31γ = 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
11.6257.41970.0490.0590.0320.99811.93.3103764
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)
11.621.6680.40.8171.0080.5810.5931.12.5

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTin-house model1.6257.4198640512096.890.166250.1650.180.190390.2RANDOM32.329
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]
2.88-0.21-0.54-1.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.091
r_dihedral_angle_4_deg16.357
r_dihedral_angle_3_deg13.318
r_long_range_B_other6.991
r_long_range_B_refined6.988
r_scangle_other5.951
r_dihedral_angle_1_deg5.18
r_scbond_it4.076
r_scbond_other4.074
r_mcangle_it3.595
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.091
r_dihedral_angle_4_deg16.357
r_dihedral_angle_3_deg13.318
r_long_range_B_other6.991
r_long_range_B_refined6.988
r_scangle_other5.951
r_dihedral_angle_1_deg5.18
r_scbond_it4.076
r_scbond_other4.074
r_mcangle_it3.595
r_mcangle_other3.595
r_mcbond_it2.69
r_mcbond_other2.69
r_angle_refined_deg1.817
r_angle_other_deg1.079
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms5260
Nucleic Acid Atoms
Solvent Atoms500
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing