8Q17

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% v/v PPG400
Crystal Properties
Matthews coefficientSolvent content
2.244.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.45α = 90
b = 109.846β = 90
c = 57.59γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2018-09-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.70988.46920.99512.611.656541
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)
11.7091.770.764

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 REPLACEMENTTHROUGHOUT1.7188.4553377273891.280.197420.195310.23869RANDOM33.171
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]
-0.57-0.621.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.537
r_dihedral_angle_4_deg20.608
r_dihedral_angle_3_deg14.37
r_long_range_B_refined7.564
r_long_range_B_other7.564
r_dihedral_angle_1_deg6.239
r_scangle_other5.945
r_mcangle_it4.297
r_mcangle_other4.297
r_scbond_it3.988
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.537
r_dihedral_angle_4_deg20.608
r_dihedral_angle_3_deg14.37
r_long_range_B_refined7.564
r_long_range_B_other7.564
r_dihedral_angle_1_deg6.239
r_scangle_other5.945
r_mcangle_it4.297
r_mcangle_other4.297
r_scbond_it3.988
r_scbond_other3.987
r_mcbond_it3.066
r_mcbond_other3.064
r_angle_refined_deg1.973
r_angle_other_deg1.103
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.011
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 Atoms4321
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms118

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing