5G57 | pdb_00005g57

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-001


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 PH 6.5; VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 4 DEGREES
Crystal Properties
Matthews coefficientSolvent content
2.7455.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.42α = 90
b = 115.09β = 108.08
c = 68.76γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MCRL2016-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I03DiamondI03

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
11.7379.7799.30.0513.43.388979
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)
11.731.7799.60.841.32.9

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.7379.7784604437599.30.160260.159060.170.183290.19RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_3_deg13.089
r_dihedral_angle_4_deg11.511
r_long_range_B_refined7.012
r_long_range_B_other7.012
r_dihedral_angle_1_deg5.252
r_scangle_other5.126
r_scbond_it3.341
r_scbond_other3.34
r_mcangle_it3.172
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.131
r_dihedral_angle_3_deg13.089
r_dihedral_angle_4_deg11.511
r_long_range_B_refined7.012
r_long_range_B_other7.012
r_dihedral_angle_1_deg5.252
r_scangle_other5.126
r_scbond_it3.341
r_scbond_other3.34
r_mcangle_it3.172
r_mcangle_other3.171
r_mcbond_it2.192
r_mcbond_other2.191
r_angle_refined_deg1.494
r_angle_other_deg0.998
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms496
Heterogen Atoms179

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling