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Crystal Structure of M. tuberculosis LD-transpeptidase type 2 with Modified Catalytic Cysteine (C354)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M Hepes (pH 7.5), 1 M succinic Acid, 1% (w/v) PEG MME 2000, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.56 65.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.044 α = 90 b = 121.223 β = 90 c = 122.884 γ = 90
Symmetry Space Group I 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RIGAKU SATURN 944+ 2009-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE OTHER 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 20 100 0.152 4.5 7.2 22155
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 2.8 2.85 99.5 0.555 6.2 1094
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.8 19.84 22139 1127 99.83 0.1904 0.1867 0.1825 0.2582 0.2515 RANDOM 21.8225
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] 2.18 -0.85 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.962 r_dihedral_angle_4_deg 20.19 r_dihedral_angle_3_deg 18.267 r_dihedral_angle_1_deg 10.15 r_scangle_it 4.01 r_scbond_it 2.333 r_angle_refined_deg 1.73 r_mcangle_it 1.443 r_mcbond_it 0.729 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.962 r_dihedral_angle_4_deg 20.19 r_dihedral_angle_3_deg 18.267 r_dihedral_angle_1_deg 10.15 r_scangle_it 4.01 r_scbond_it 2.333 r_angle_refined_deg 1.73 r_mcangle_it 1.443 r_mcbond_it 0.729 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4029 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 14
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SHARP phasing