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Crystal structure of a probable enoyl-CoA hydratase/isomerase from Mycobacterium abscessus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H81
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 MyabA.00305.a.A1 at 34.6 mg/mL against JCSG+ screen condition B12, 0.2 M potassium citrate, 20% PEG 3350 with 25% ethylene glycol as cryo-protection reagent, crystal tracking ID 219708b12, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.08 40.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.09 α = 90 b = 131.65 β = 90 c = 148.71 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2011-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.35 50 98.4 0.134 13.16 7 66204 65136 -3 29.276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.41 99.9 0.469 4.3 6.8 4840
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 3h81 2.35 50 64902 3299 98.05 0.2054 0.2026 0.203 0.2578 0.258 RANDOM 20.4687
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] 0.81 0.63 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.971 r_dihedral_angle_4_deg 16.57 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_1_deg 6.048 r_scangle_it 3.092 r_scbond_it 1.962 r_angle_refined_deg 1.402 r_mcangle_it 1.086 r_mcbond_it 0.592 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.971 r_dihedral_angle_4_deg 16.57 r_dihedral_angle_3_deg 14.87 r_dihedral_angle_1_deg 6.048 r_scangle_it 3.092 r_scbond_it 1.962 r_angle_refined_deg 1.402 r_mcangle_it 1.086 r_mcbond_it 0.592 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11634 Nucleic Acid Atoms Solvent Atoms 466 Heterogen Atoms 39
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction