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Structural Basis for Substrate Fatty-Acyl Chain Specificity: Crystal Structure of Human Very-Long-Chain Acyl-CoA Dehydrogenase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 0.1 M HEPES, 17.6% PEG 2000, 0.047 M MgCl2, 5% glycerol, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.37 48.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.616 α = 90 b = 107.879 β = 90 c = 149.776 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 IMAGE PLATE RIGAKU RAXIS IV++ 2006-05-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD 2006-05-14 M SINGLE WAVELENGTH 3 1 x-ray 100 CCD 2006-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.5419 2 SYNCHROTRON APS BEAMLINE 19-ID 1.0083 APS 19-ID 3 SYNCHROTRON APS BEAMLINE 5ID-B 1.1405 APS 5ID-B
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 1,2,3 1.91 50 98.8 0.079 15.2 7.6 46776
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) 1.91 1.98 98.4 0.532 6.7 4630
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIRAS THROUGHOUT 1.91 30.69 46738 2371 98.65 0.162 0.159 0.1605 0.216 0.2153 RANDOM 24.049
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] 0.1 -0.06 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.3 r_dihedral_angle_4_deg 14.36 r_dihedral_angle_3_deg 14.295 r_scangle_it 9.717 r_scbond_it 7.019 r_dihedral_angle_1_deg 6.034 r_mcangle_it 4.221 r_mcbond_it 3.728 r_angle_refined_deg 1.353 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.3 r_dihedral_angle_4_deg 14.36 r_dihedral_angle_3_deg 14.295 r_scangle_it 9.717 r_scbond_it 7.019 r_dihedral_angle_1_deg 6.034 r_mcangle_it 4.221 r_mcbond_it 3.728 r_angle_refined_deg 1.353 r_nbtor_refined 0.309 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.214 r_symmetry_hbond_refined 0.168 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.113 r_bond_refined_d 0.014 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4225 Nucleic Acid Atoms Solvent Atoms 441 Heterogen Atoms 76
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction