5LB1

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with thionitrobenzoate (TNB) adduct at the active site cysteine-354


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4HUC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.1M MES/Imidazol pH 6.5 0.02M of each carboxylic acid (sodium formate, ammonium acetate, tri-sodium citrate, sodium potassium DL-tartrate, sodium oxamate) 10% PEG 20000 20%PEGMME 550
Crystal Properties
Matthews coefficientSolvent content
2.652.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.368α = 68.84
b = 53.91β = 75.03
c = 57.174γ = 88.64
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2MPt coated mirrors2014-11-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.5551.495.30.0650.9979.72794621.711.2
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)
11.551.5789.60.3791.72

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 REPLACEMENTTHROUGHOUT4HUC1.5551.475507395395.350.149810.147460.19415RANDOM14.581
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]
-0.20.12-0.03-0.06-0.120.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.654
r_sphericity_free29.813
r_dihedral_angle_4_deg17.177
r_dihedral_angle_3_deg11.82
r_sphericity_bonded8.58
r_dihedral_angle_1_deg5.914
r_rigid_bond_restr4.279
r_angle_refined_deg1.453
r_angle_other_deg0.879
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.654
r_sphericity_free29.813
r_dihedral_angle_4_deg17.177
r_dihedral_angle_3_deg11.82
r_sphericity_bonded8.58
r_dihedral_angle_1_deg5.914
r_rigid_bond_restr4.279
r_angle_refined_deg1.453
r_angle_other_deg0.879
r_chiral_restr0.09
r_bond_refined_d0.011
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_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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3935
Nucleic Acid Atoms
Solvent Atoms672
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing