3ZXV

Crystal structure of Mycobacterium Tuberculosis Glutamine Synthetase in complex with tri-substituted imidazole inhibitor (4-(2-tert-butyl- 4-(6-methoxynaphthalen-2-yl)-1H-imidazol-5-yl)pyridin-2-amine) and L- methionine-S-sulfoximine phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BVCPDB ENTRY 2BVC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.8294EQUAL VOLUMES OF MOTHER LIQUOR (0.1 M MES, PH 6.8, 0.2 M MAGNESIUM CHLORIDE, 45% (V/V) PEG400) AND PROTEIN SOLUTION (13 G/L IN 0.1 M TRIS-HCL, PH 7.5, 0.125 M SODIUM CHLORIDE, 0.004 M MAGNESIUM CHLORIDE, 4%(V/V) DMSO, 0.001 M INHIBITOR, 0.004 M MSOP), HANGING-DROP, VAPOR DIFFUSION, TEMPERATURE 294K.
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 132.59α = 90
b = 227.15β = 90
c = 201.62γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
12.263099.50.0916.23.914095538.993
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)
12.262.36990.72.293.4

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2BVC2.2629.73133842711099.540.195840.195050.21055RANDOM33.361
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]
1.46-2.481.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg14.885
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg5.951
r_scangle_it2.112
r_scbond_it1.281
r_angle_refined_deg1.264
r_mcangle_it0.834
r_mcbond_it0.426
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.408
r_dihedral_angle_4_deg14.885
r_dihedral_angle_3_deg13.86
r_dihedral_angle_1_deg5.951
r_scangle_it2.112
r_scbond_it1.281
r_angle_refined_deg1.264
r_mcangle_it0.834
r_mcbond_it0.426
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other
r_mcangle_other
r_scbond_other
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 Atoms22572
Nucleic Acid Atoms
Solvent Atoms1104
Heterogen Atoms312

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing