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Crystal structure of Mycobacterium tuberculosis dethiobiotin synthetase in complex with fragment analogue 8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 1.2 - 1.7 M ammonium sulfate, 0.1 M Tris pH 8, 10-15% glycerol
Crystal Properties Matthews coefficient Solvent content 2.35 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.401 α = 90 b = 104.342 β = 90 c = 154.297 γ = 90
Symmetry Space Group P 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 ADSC QUANTUM 210r 2017-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.9537 Australian Synchrotron MX1
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 1.99 46.13 99.7 0.087 0.093 0.035 0.999 13.1 7.3 61199 28.99
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 1.99 2.04 96.4 0.771 0.831 0.308 0.871 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6CVE 1.989 46.132 0.32 60924 3108 99.42 0.1874 0.1849 0.2303 0.2085 30.7984
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 19.839 f_angle_d 0.861 f_chiral_restr 0.05 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6292 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 140
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction