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Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with cyanamide analogue 31
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RRM 6RRM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M Ammonium nitrate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.88 57.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.25 α = 90 b = 94.261 β = 92.69 c = 75.667 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 XE 16M 2020-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 61.18 99.79 0.136 0.147 0.057 0.89 8.9 6.9 74669
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 98.36 0.782 0.846 0.319 0.865 1.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6RRM 2.3 61.18 1.38 74669 3867 99.41 0.2108 0.2087 0.2121 0.248 0.2478 45.3178
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5209 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 41
Software Software Software Name Purpose XDS data reduction xia2 data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction