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Crystal Structure of Enoyl-[acyl-carrier-protein] reductase InhA from Mycobacterium abscessus in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7KLI apo structure, PDB code 7KLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.27 287 Optimization condition around RigakuReagents JCSG+ E1: 100mM Sodium cacodylate / HCl pH 6.27, 1090mM sodium citrate tribasic: MyabA.00710.a.B1.PS38577 at 23.06mg/ml + 4mM NAD: tray: 319064 c9: cryo: 20% EG + 4mM NAD: puck: ZXC1-5.
Crystal Properties Matthews coefficient Solvent content 3.48 64.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.66 α = 90 b = 92.63 β = 118.318 c = 98.13 γ = 90
Symmetry Space Group C 1 2 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 CCD RIGAKU SATURN 944+ 2020-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.85 50 99.7 0.074 0.076 0.999 25.53 16.298 138659 33.792
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 99.3 0.593 0.627 0.905 3.14 9.292
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE apo structure, PDB code 7KLI 1.85 46.31 1.35 138636 2015 99.92 0.19 0.1896 0.1895 0.2185 0.2181 0 31.79
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 11.6636 f_angle_d 0.9543 f_chiral_restr 0.0596 f_plane_restr 0.01 f_bond_d 0.0082
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7867 Nucleic Acid Atoms Solvent Atoms 866 Heterogen Atoms 188
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction PHASER phasing PHENIX model building Coot model building