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Crystal Structure of Enoyl-[acyl-carrier-protein] reductase from Mycobacterium avium with bound NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H7I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 287 MyavA.00170.a.B1.PS38585 @ 20.93 mg/mL, incubated with 5 mM NAD, mixed 0.4uL protein ligand complex + 0.4uL JCSG+ (D10): 40% (v/v) PEG300, 100 mM Sodium Cacodylate/ HCl pH 6.5, 200 mM Calcium acetate. Tray ID: 310540 D10, puck: ixz5-8
Crystal Properties Matthews coefficient Solvent content 3.08 60.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.32 α = 90 b = 95.32 β = 90 c = 139.59 γ = 120
Symmetry Space Group P 62 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 CCD RAYONIX MX-300 Beryllium Lenses 2019-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.65 41.275 99.8 0.056 0.058 1 32.41 17.614 45632 27.223
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 1.65 1.69 100 0.551 0.57 0.982 4.99 14.892
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 2H7I 1.65 41.275 1.35 45601 2009 99.86 0.1427 0.1416 0.1422 0.1689 0.1685 random, 0 24.4317
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1992 Nucleic Acid Atoms Solvent Atoms 348 Heterogen Atoms 85
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing