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Structure of DNA ligase A from Mycobacterium tuberculosis bound to NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SGI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 Morpheus A12 +4 mM NAD (BSI1606) 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 0.03 M of each divalent cation (0.3 M magnesium chloride, 0.3 M calcium chloride), 0.1 M bicine/Trizma base pH 8.5, cryo: direct, MytuD.17946.a.B2.PS38127 at 21.72mg/ml, cryo: direct, tray: 289017A12, puck ydo7-6
Crystal Properties Matthews coefficient Solvent content 2.39 48.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.94 α = 96.22 b = 63.81 β = 89.55 c = 120.73 γ = 111.97
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 RAYONIX MX-300 2018-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.05 44.59 98.1 0.066 0.076 0.998 14.18 3.937 86267 37.983
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 97 0.593 0.685 0.784 2.39 3.982
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 3SGI 2.05 44.59 1.98 86257 1912 98.14 0.1691 0.1683 0.1697 0.2059 0.2063 39.4182
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 9912 Nucleic Acid Atoms Solvent Atoms 807 Heterogen Atoms 227
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing