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Crystal structure of mycolic acid transporter MmpL3 from Mycobacterium smegmatis complexed with indolcarboxamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OR2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 20mM HEPES pH7.5, 150mM NaCl, 0.05% DDM, 1.17mM Indolecarboxyamide, 2% DMSO
Crystal Properties Matthews coefficient Solvent content 4.23 70.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.289 α = 90 b = 105.34 β = 114.521 c = 89.468 γ = 90
Symmetry Space Group P 1 21 1
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 2023-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 46.94 99.91 0.126 0.024 0.996 12.4 25.9 77682 58.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.18 98.59 0.573 0.744 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.15 43.42 1.36 77553 3855 99.75 0.217 0.2158 0.2178 0.2424 0.2439 82.22
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 9.5918 f_angle_d 0.5678 f_chiral_restr 0.039 f_plane_restr 0.005 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5535 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 231
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing