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Crystal Structure of Mycobacterium smegmatis MshC in Complex with Compound 7d
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, SITTING DROP 8.5 293 Holo protein at 10 mg/mL in 10 mM Tris-HCl pH 7, 100 mM NaCl and 2.5 mM 2-mercaptoethanol was mixed with 1 mM compound 7d and 1 mM TCEP (final concentrations) and incubated on ice for 1 hr. Crystals of MshC in complex with compound 7d were grown in the Morpheus screen by dispensing droplets comprised of 300 nL protein mixture and 150 nL reservoir solution containing PEG550MME 20% (v/v), PEG20000 10% (w/v), Morpheus divalent 60 mM and Morpheus buffer system 3 pH 8.5.
Crystal Properties Matthews coefficient Solvent content 4.69 73.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.113 α = 90 b = 168.113 β = 90 c = 52.3 γ = 120
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 2021-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.774900 ESRF ID23-1
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 2.77 145.59 100 0.098 0.101 0.023 0.993 17.5 20.1 21805
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 2.77 2.92 100 1.387 1.421 0.312 0.898 20.6
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 3C8Z 2.77 55.03 1.38 21782 1132 99.9 0.2026 0.2001 0.2521 0.2671
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 5.745 f_angle_d 0.772 f_chiral_restr 0.049 f_plane_restr 0.009 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3181 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 23
Software Software Software Name Purpose Aimless data scaling PHENIX refinement XDS data reduction PHASER phasing