5G5V

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-038


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4I15PDB ENTRY 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 PH 6.5; VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 4 DEGREES
Crystal Properties
Matthews coefficientSolvent content
3.3763.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.69α = 90
b = 114.781β = 109.4
c = 64.009γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXELCRL2015-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04DiamondI04

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
11.888.5897.90.17.13.290889
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)
11.81.83970.62.13.2

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4I151.888.5886430444997.720.177480.176370.19872RANDOM
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_deg33.539
r_dihedral_angle_3_deg13.123
r_dihedral_angle_4_deg12.081
r_long_range_B_refined5.453
r_long_range_B_other5.453
r_dihedral_angle_1_deg5.04
r_scangle_other2.767
r_mcangle_it2.077
r_mcangle_other2.077
r_scbond_it1.683
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.539
r_dihedral_angle_3_deg13.123
r_dihedral_angle_4_deg12.081
r_long_range_B_refined5.453
r_long_range_B_other5.453
r_dihedral_angle_1_deg5.04
r_scangle_other2.767
r_mcangle_it2.077
r_mcangle_other2.077
r_scbond_it1.683
r_scbond_other1.683
r_angle_refined_deg1.336
r_mcbond_it1.222
r_mcbond_other1.222
r_angle_other_deg0.997
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms5280
Nucleic Acid Atoms
Solvent Atoms445
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing