5I7R

Mycobacterium tuberculosis CysM in complex with the Urea-scaffold inhibitor 2 [3-(3-([1,1'-biphenyl]-3-yl)ureido)benzoic acid]


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52930.2M NH4-acetate, 0.1M BT pH 5.5, 25% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.448.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.17α = 90
b = 86.487β = 90
c = 101.584γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6Mmirrors2014-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97242ESRFID23-1

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
11.7365.8698.30.04119.64.565578225.7
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)
11.731.8198.80.71724.3

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 REPLACEMENTTHROUGHOUT3dki1.7365.8562228330897.810.175490.173810.20671RANDOM33.351
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]
2.99-1.61-1.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.092
r_dihedral_angle_4_deg18.162
r_dihedral_angle_3_deg13.702
r_long_range_B_refined5.961
r_long_range_B_other5.961
r_dihedral_angle_1_deg5.825
r_scangle_other4.52
r_mcangle_it3.201
r_mcangle_other3.201
r_scbond_it3.009
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.092
r_dihedral_angle_4_deg18.162
r_dihedral_angle_3_deg13.702
r_long_range_B_refined5.961
r_long_range_B_other5.961
r_dihedral_angle_1_deg5.825
r_scangle_other4.52
r_mcangle_it3.201
r_mcangle_other3.201
r_scbond_it3.009
r_scbond_other3.009
r_mcbond_it2.361
r_mcbond_other2.287
r_angle_refined_deg1.608
r_angle_other_deg0.873
r_chiral_restr0.094
r_bond_refined_d0.013
r_gen_planes_refined0.007
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 Atoms4682
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing