5IW8

Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 4 [5-(3-([1,1'-Biphenyl]-3-yl)ureido)-2-hydroxybenzoic acid]


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M MES 6 pH 20 %w/v PEG 6K 0.2 M NH4Cl
Crystal Properties
Matthews coefficientSolvent content
2.1342.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.164α = 90
b = 87.883β = 90
c = 100.781γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6MSi mirrors2015-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97625ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.0455.9599.50.1678.35.5385651.920.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.042.1597.30.8191.95.7

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3DKI2.0455.9536652185799.360.18710.184460.23714RANDOM29.623
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]
-0.6-0.070.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.615
r_dihedral_angle_4_deg17.25
r_dihedral_angle_3_deg15.18
r_dihedral_angle_1_deg5.904
r_angle_refined_deg1.487
r_angle_other_deg0.835
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.615
r_dihedral_angle_4_deg17.25
r_dihedral_angle_3_deg15.18
r_dihedral_angle_1_deg5.904
r_angle_refined_deg1.487
r_angle_other_deg0.835
r_chiral_restr0.079
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4626
Nucleic Acid Atoms
Solvent Atoms446
Heterogen Atoms53

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing