6FV9 | pdb_00006fv9

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-007


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 pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6653.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.203α = 90
b = 114.619β = 108.36
c = 68.387γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2018-02-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.91587DiamondI04-1

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
12.47979.47398.10.3770.4490.2420.9164.43.329623
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)
12.4792.522981.2921.5280.810.3661.83.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4I152.4879.4728048144197.640.208290.205920.210.25360.26RANDOM23.119
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]
2.83-0.4-1.74-0.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.663
r_dihedral_angle_4_deg17.079
r_dihedral_angle_3_deg16.333
r_long_range_B_refined5.977
r_long_range_B_other5.977
r_dihedral_angle_1_deg5.15
r_scangle_other2.251
r_mcangle_it2.057
r_mcangle_other2.057
r_angle_refined_deg1.442
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.663
r_dihedral_angle_4_deg17.079
r_dihedral_angle_3_deg16.333
r_long_range_B_refined5.977
r_long_range_B_other5.977
r_dihedral_angle_1_deg5.15
r_scangle_other2.251
r_mcangle_it2.057
r_mcangle_other2.057
r_angle_refined_deg1.442
r_scbond_it1.319
r_scbond_other1.318
r_mcbond_it1.201
r_mcbond_other1.199
r_angle_other_deg1.01
r_chiral_restr0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms373
Heterogen Atoms102

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
autoPROCdata collection
PHASERphasing