8Q0T

Identification and optimisation of novel inhibitors of the Polyketide synthetase 13 thioesterase domain with antitubercular activity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V3W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2911.65M AmSO4, 0.1M Tris, pH 8.5, 3% PPG 400
Crystal Properties
Matthews coefficientSolvent content
2.1943.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.273α = 90
b = 110.247β = 90
c = 57.862γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.968DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.868.9197.10.0960.110.99912.67.151471
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8499.90.6257.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.868.9148824256596.80.188050.186110.2242RANDOM30.426
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]
-0.03-0.720.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.569
r_dihedral_angle_4_deg22.902
r_dihedral_angle_3_deg15.924
r_long_range_B_refined6.937
r_long_range_B_other6.929
r_dihedral_angle_1_deg6.33
r_scangle_other5.463
r_mcangle_it3.785
r_mcangle_other3.784
r_scbond_it3.726
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.569
r_dihedral_angle_4_deg22.902
r_dihedral_angle_3_deg15.924
r_long_range_B_refined6.937
r_long_range_B_other6.929
r_dihedral_angle_1_deg6.33
r_scangle_other5.463
r_mcangle_it3.785
r_mcangle_other3.784
r_scbond_it3.726
r_scbond_other3.725
r_mcbond_it2.727
r_mcbond_other2.726
r_angle_refined_deg1.808
r_angle_other_deg1.097
r_chiral_restr0.118
r_bond_refined_d0.018
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 Atoms4290
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing