2BVC

Crystal structure of Mycobacterium tuberculosis glutamine synthetase in complex with a transition state mimic


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HTOPDB ENTRY 1HTO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.830% PEG400, 0.1M MES PH6.8, 200 MM MGCL2, pH 6.80
Crystal Properties
Matthews coefficientSolvent content
2.550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.261α = 90
b = 229.457β = 90
c = 203.167γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2004-08-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.12089.60.0613.23.51604323
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)
12.12.1769.10.342.42.1

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 1HTO2.120152255801189.20.1930.1910.23RANDOM25.35
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]
1.27-1.470.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.518
r_dihedral_angle_4_deg16.097
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.637
r_scangle_it1.406
r_angle_refined_deg1.161
r_scbond_it0.91
r_mcangle_it0.637
r_mcbond_it0.372
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.518
r_dihedral_angle_4_deg16.097
r_dihedral_angle_3_deg13.776
r_dihedral_angle_1_deg5.637
r_scangle_it1.406
r_angle_refined_deg1.161
r_scbond_it0.91
r_mcangle_it0.637
r_mcbond_it0.372
r_nbtor_refined0.299
r_nbd_refined0.185
r_symmetry_vdw_refined0.156
r_symmetry_hbond_refined0.119
r_xyhbond_nbd_refined0.104
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms621
Heterogen Atoms276

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing