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Crystal structure of human very long chain acyl-CoA dehydrogenase (ACADVL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIF PDB ENTRY 2JIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 15% PEG3350, 0.1M SODIUM SUCCINATE PH7.0, pH 7.00
Crystal Properties Matthews coefficient Solvent content 2.41 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.001 α = 90 b = 108.173 β = 90 c = 149.731 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 100 CCD MARRESEARCH 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.45 47.56 100 0.08 13.8 7.4 107669 16.81
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 1.45 1.53 100 0.78 2.2 7
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 PDB ENTRY 2JIF 1.45 45 102266 5352 100 0.149 0.148 0.1577 0.17 0.1777 RANDOM 14.74
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] 0.7 -0.31 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.915 r_dihedral_angle_4_deg 14.892 r_dihedral_angle_3_deg 11.757 r_scangle_it 6.803 r_dihedral_angle_1_deg 5.082 r_scbond_it 4.363 r_mcangle_it 2.923 r_mcbond_it 2.06 r_angle_refined_deg 1.33 r_angle_other_deg 0.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.915 r_dihedral_angle_4_deg 14.892 r_dihedral_angle_3_deg 11.757 r_scangle_it 6.803 r_dihedral_angle_1_deg 5.082 r_scbond_it 4.363 r_mcangle_it 2.923 r_mcbond_it 2.06 r_angle_refined_deg 1.33 r_angle_other_deg 0.798 r_symmetry_vdw_other 0.313 r_nbd_refined 0.228 r_nbd_other 0.2 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.176 r_symmetry_vdw_refined 0.145 r_nbtor_other 0.094 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4275 Nucleic Acid Atoms Solvent Atoms 504 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing