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Crystal structure of the Mycobacterium tuberculosis L,D-transpeptidase-2 (LdtMt2) BC-module with thionitrobenzoate (TNB) adduct at the active site cysteine-354
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HUC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.1M 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 coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.368 α = 68.84 b = 53.91 β = 75.03 c = 57.174 γ = 88.64
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M Pt coated mirrors 2014-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 51.4 95.3 0.065 0.997 9.7 2 79462 1.7 11.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.57 89.6 0.379 1.7 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4HUC 1.55 51.4 75507 3953 95.35 0.14981 0.14746 0.1602 0.19415 0.2028 RANDOM 14.581
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] -0.2 0.12 -0.03 -0.06 -0.12 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.654 r_sphericity_free 29.813 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 11.82 r_sphericity_bonded 8.58 r_dihedral_angle_1_deg 5.914 r_rigid_bond_restr 4.279 r_angle_refined_deg 1.453 r_angle_other_deg 0.879 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.654 r_sphericity_free 29.813 r_dihedral_angle_4_deg 17.177 r_dihedral_angle_3_deg 11.82 r_sphericity_bonded 8.58 r_dihedral_angle_1_deg 5.914 r_rigid_bond_restr 4.279 r_angle_refined_deg 1.453 r_angle_other_deg 0.879 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 3935 Nucleic Acid Atoms Solvent Atoms 672 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing