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Crystal structure of a probable acyl CoA dehydrogenase from Mycobacterium abscessus ATCC 19977 / DSM 44196
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 290 Internal tracking number 220102B12 JCSG screen condition B12: 20% PEG3350, 0.2 M potassium citrate. MyabA.00247.g.A1 PS 00948 at 39.2 mg/ml, pH 7.0, vapor diffusion, sitting drop, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.57 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.25 α = 90 b = 121.12 β = 90 c = 172.09 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 MARMOSAIC 300 mm CCD 2011-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.5 49.52 99.9 0.084 10.96 5.2 62386 62349 -3 60.585
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 2.5 2.56 100 0.644 2.3 5.6 4550
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 3oib 2.5 49.52 62386 62184 4843 99.67 0.212 0.212 0.208 0.2138 0.259 0.2599 RANDOM 59.284
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] 0.33 -0.91 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 18.589 r_dihedral_angle_3_deg 15.962 r_dihedral_angle_1_deg 6.111 r_scangle_it 2.904 r_scbond_it 1.806 r_angle_refined_deg 1.588 r_mcangle_it 1.132 r_angle_other_deg 1.004 r_mcbond_it 0.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.269 r_dihedral_angle_4_deg 18.589 r_dihedral_angle_3_deg 15.962 r_dihedral_angle_1_deg 6.111 r_scangle_it 2.904 r_scbond_it 1.806 r_angle_refined_deg 1.588 r_mcangle_it 1.132 r_angle_other_deg 1.004 r_mcbond_it 0.627 r_mcbond_other 0.155 r_chiral_restr 0.09 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11024 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 218
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction