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Crystal structure of LdtMt2 from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DUJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 277 0.2 M Ammonium nitrate pH 6.3, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.87 57.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.95 α = 90 b = 93.92 β = 93.03 c = 75.57 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 PILATUS 2M 2018-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97952 Diamond I04
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 1.51 33.79 99.9 0.0748 0.081 0.032 0.99 12.03 6.5 132783 21.2079757645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.54 100 0.685 0.56 1.1 6.7
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 FREE R-VALUE 5DUJ 1.51000183032 33.7871482655 1.34349787152 132704 6726 99.8082115539 0.181402239935 0.180194769066 0.1813 0.203826681086 0.2056 30.1701442648
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.6630625072 f_angle_d 0.99258571886 f_chiral_restr 0.0633409903721 f_bond_d 0.00859965640507 f_plane_restr 0.00711880568372
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5237 Nucleic Acid Atoms Solvent Atoms 828 Heterogen Atoms 78
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling SHELXD phasing