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Crystal structure of acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to flavin adenine dinucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DVL 2dvl molecule a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 69.7 mg/mL protein against PACT screen condition e11, 0.2 M Na Citrate, 20% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 215726e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.65 α = 90 b = 99.23 β = 90 c = 171.49 γ = 90
Symmetry Space Group I 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 2010-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 98.8 0.063 22.1 8.6 34384 33958 -3 44.057
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 96.9 0.339 6.6 8.8 2504
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2dvl molecule a 2.35 19.69 33892 1697 98.57 0.194 0.191 0.24 0.2138 RANDOM 59.617
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] -3.08 -0.35 3.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.436 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_3_deg 16.414 r_dihedral_angle_1_deg 5.445 r_scangle_it 3.324 r_scbond_it 2.047 r_angle_refined_deg 1.453 r_mcangle_it 1.219 r_mcbond_it 0.639 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.436 r_dihedral_angle_4_deg 16.537 r_dihedral_angle_3_deg 16.414 r_dihedral_angle_1_deg 5.445 r_scangle_it 3.324 r_scbond_it 2.047 r_angle_refined_deg 1.453 r_mcangle_it 1.219 r_mcbond_it 0.639 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5447 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 54
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction