6RFN | pdb_00006rfn

Crystal structure of T. brucei PDE-B1 catalytic domain with inhibitor NPD-1018


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
2.6854.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.713α = 90
b = 116.081β = 108.26
c = 68.669γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-28MSINGLE 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
12.2865.2198.30.0780.0920.0490.99610.73.437946
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)
12.282.2996.50.5510.6550.350.8642.33.3

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 REPLACEMENTTHROUGHOUT4I152.2965.2136118182198.350.166890.164030.170.222270.22RANDOM47.125
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]
4.94-0.611.2-4.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.38
r_dihedral_angle_3_deg16.789
r_dihedral_angle_4_deg15.942
r_long_range_B_other9.266
r_long_range_B_refined9.265
r_scangle_other7.344
r_dihedral_angle_1_deg6.685
r_mcangle_other6.266
r_mcangle_it6.264
r_scbond_it5.097
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.38
r_dihedral_angle_3_deg16.789
r_dihedral_angle_4_deg15.942
r_long_range_B_other9.266
r_long_range_B_refined9.265
r_scangle_other7.344
r_dihedral_angle_1_deg6.685
r_mcangle_other6.266
r_mcangle_it6.264
r_scbond_it5.097
r_scbond_other5.096
r_mcbond_it4.355
r_mcbond_other4.347
r_angle_refined_deg1.683
r_angle_other_deg1.375
r_chiral_restr0.082
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d0.001
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 Atoms339
Heterogen Atoms114

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing