5LBG

Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with faropenem-derived 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 DROP4.252930.1M Citrate pH 4.25 17.5% PEG6K, ligand soak at pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.3848.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.062α = 90
b = 91.362β = 103.59
c = 67.55γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6Mmirrors2016-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97624ESRFID29

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
11.5465.6699.10.0290.99914.63777802.121.7
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)
11.541.57990.4642.13

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 REPLACEMENTTHROUGHOUT4HUC1.5465.6673847383798.970.177230.175740.20625RANDOM24.795
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]
0.040.150.74-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.553
r_dihedral_angle_4_deg20.205
r_dihedral_angle_3_deg14.143
r_long_range_B_refined4.922
r_long_range_B_other4.814
r_dihedral_angle_1_deg4.702
r_scangle_other3.504
r_scbond_it2.295
r_scbond_other2.295
r_mcangle_it2.162
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.553
r_dihedral_angle_4_deg20.205
r_dihedral_angle_3_deg14.143
r_long_range_B_refined4.922
r_long_range_B_other4.814
r_dihedral_angle_1_deg4.702
r_scangle_other3.504
r_scbond_it2.295
r_scbond_other2.295
r_mcangle_it2.162
r_mcangle_other2.162
r_angle_refined_deg1.759
r_mcbond_it1.458
r_mcbond_other1.453
r_angle_other_deg1.056
r_chiral_restr0.105
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3980
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing