8Q0U

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 DROP2910.1M Tris-HCl pH 8.5, 1.8 M Ammonium sulfate, 3% PPG400
Crystal Properties
Matthews coefficientSolvent content
2.2445.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.565α = 90
b = 108.606β = 90
c = 57.525γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 9M2019-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9159DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.868.1793.80.934.17.148490
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)
11.81.840.54

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 REPLACEMENTTHROUGHOUT1.868.1745754243093.360.191460.189230.23459RANDOM30.296
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]
0.49-10.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.966
r_dihedral_angle_4_deg20.236
r_dihedral_angle_3_deg14.28
r_long_range_B_refined7.361
r_long_range_B_other7.242
r_dihedral_angle_1_deg6.061
r_scangle_other5.339
r_mcangle_other3.703
r_mcangle_it3.702
r_scbond_it3.533
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.966
r_dihedral_angle_4_deg20.236
r_dihedral_angle_3_deg14.28
r_long_range_B_refined7.361
r_long_range_B_other7.242
r_dihedral_angle_1_deg6.061
r_scangle_other5.339
r_mcangle_other3.703
r_mcangle_it3.702
r_scbond_it3.533
r_scbond_other3.526
r_mcbond_it2.679
r_mcbond_other2.676
r_angle_refined_deg1.86
r_angle_other_deg1.059
r_chiral_restr0.111
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 Atoms4298
Nucleic Acid Atoms
Solvent Atoms412
Heterogen Atoms78

Software

Software
Software NamePurpose
REFMACrefinement
autoPROCdata reduction
SCALAdata scaling
PHASERphasing