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Mycobacterium tuberculosis toxin MazF-mt6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MDX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 50 mM sodium cacodylate pH 6.0, 10 mM magnesium chloride, 1.05 M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 5.32 76.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.22 α = 90 b = 105.22 β = 90 c = 144.44 γ = 120
Symmetry Space Group P 64 2 2
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 6M-F 2015-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97920 APS 24-ID-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 49 98 12 6.5 13353
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 4mdx 2.7 49.433 1.35 13352 681 98.43 0.2401 0.2391 0.2434 0.2551 0.2554
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 12.947 f_angle_d 0.55 f_chiral_restr 0.047 f_plane_restr 0.005 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1514 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling