☰ Navigation Tabs
Crystal Structure of Mycobacterium smegmatis MshC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 Holo protein at 10 mg/mL in 10 mM Tris pH 7, 100 mM NaCl, 2.5 mM 2-mercaptoethanol was mixed with 25 mM CaCl2, 25 mM MgCl2, PEG8000 5-8% (w/v), Morpheus buffer system 2 pH 7.1, ethylene glycol 20% (v/v) in a 1:1 ratio. Suitable crystals were immersed in mother liquor supplemented with 22% (v/v) ethylene glycol as a cryoprotectant and flash frozen in liquid nitrogen for subsequent data collection.
Crystal Properties Matthews coefficient Solvent content 3.16 61.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.81 α = 90 b = 69.81 β = 90 c = 236.011 γ = 90
Symmetry Space Group P 41 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 EIGER X 16M 2019-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.911648 SOLEIL PROXIMA 1
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 2.41 69.81 100 0.172 0.175 0.034 0.999 15.3 26.1 23600
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 2.41 2.54 100 2.385 2.431 0.468 0.778 26.7
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 THROUGHOUT 3C8Z 2.41 48.32 1.35 23514 1211 99.96 0.2077 0.2061 0.2105 0.2378 0.2403
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 4.851 f_angle_d 0.642 f_chiral_restr 0.043 f_plane_restr 0.008 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3122 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 2
Software Software Software Name Purpose Aimless data scaling PHENIX refinement XDS data reduction PHASER phasing