5I7O

Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 7 [3-(3-(4-Chlorophenyl)ureido)benzoic acid]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DKI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62930.1M MES pH 6.0, 0.2 M MgCl2, 25% (W/Vol) PEG6000
Crystal Properties
Matthews coefficientSolvent content
2.5752

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.301α = 93.71
b = 75.849β = 108.43
c = 79.303γ = 107.87
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2014-08-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91843BESSY14.1

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
12.4974.0397.60.1257.42.3454152
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)
12.492.5890.20.53322.2

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 REPLACEMENTTHROUGHOUT3dki2.4974.0343105229097.590.201780.198730.25887RANDOM34.772
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]
-3.28-0.16-0.842.98-1.91.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.96
r_dihedral_angle_3_deg17.297
r_dihedral_angle_4_deg16.387
r_dihedral_angle_1_deg6.123
r_long_range_B_refined5.876
r_long_range_B_other5.876
r_scangle_other3.049
r_mcangle_it2.888
r_mcangle_other2.888
r_scbond_it1.853
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.96
r_dihedral_angle_3_deg17.297
r_dihedral_angle_4_deg16.387
r_dihedral_angle_1_deg6.123
r_long_range_B_refined5.876
r_long_range_B_other5.876
r_scangle_other3.049
r_mcangle_it2.888
r_mcangle_other2.888
r_scbond_it1.853
r_scbond_other1.853
r_mcbond_it1.783
r_mcbond_other1.783
r_angle_refined_deg1.399
r_angle_other_deg0.806
r_chiral_restr0.072
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms8837
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing