9FOY

Ternary complex of a Mycobacterium tuberculosis DNA gyrase core fusion with DNA and the inhibitor AMK32b


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293NULL
Crystal Properties
Matthews coefficientSolvent content
3.0659.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.041α = 90
b = 131.703β = 97.23
c = 96.281γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 XE 16M2022-12-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9537DiamondI04

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
12.869.231000.4140.4470.1670.9594.97.150035
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)
12.82.891001.7311.8750.7150.4146.8

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 REPLACEMENTTHROUGHOUT2.869.2347469254299.990.280590.279330.30408RANDOM41.024
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]
-2.18-0.86-2.054.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.627
r_dihedral_angle_4_deg17.609
r_dihedral_angle_3_deg16.185
r_dihedral_angle_1_deg5.441
r_long_range_B_refined1.857
r_long_range_B_other1.857
r_angle_other_deg1.22
r_angle_refined_deg1.148
r_mcangle_it0.466
r_mcangle_other0.466
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.627
r_dihedral_angle_4_deg17.609
r_dihedral_angle_3_deg16.185
r_dihedral_angle_1_deg5.441
r_long_range_B_refined1.857
r_long_range_B_other1.857
r_angle_other_deg1.22
r_angle_refined_deg1.148
r_mcangle_it0.466
r_mcangle_other0.466
r_scangle_other0.366
r_mcbond_it0.248
r_mcbond_other0.248
r_scbond_it0.187
r_scbond_other0.187
r_chiral_restr0.068
r_bond_refined_d0.004
r_gen_planes_refined0.003
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 Atoms11438
Nucleic Acid Atoms814
Solvent Atoms
Heterogen Atoms64

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing