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Crystal structure of the apo acyl-CoA dehydrogenase FadE2 (PA0508) from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6KPT experimental model PDB 6IJC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293.15 0.1 M Sodium acetate pH 4.6, 30% (v/v) PEG 300
Crystal Properties Matthews coefficient Solvent content 2.24 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.851 α = 90 b = 64.396 β = 90 c = 286.967 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 PIXEL DECTRIS EIGER2 X 16M 2021-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.94 64.4 100 0.476 0.093 0.995 6.1 26.7 86018 22.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.97 98.5 8.337 8.529 1.788 0.305 0.4 22.5
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 MOLECULAR REPLACEMENT THROUGHOUT 1.94 62.91 81637 4229 99.87 0.20568 0.20279 0.2094 0.26001 0.2605 RANDOM 33.564
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] -0.92 2.48 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_4_deg 17.695 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_1_deg 5.962 r_long_range_B_refined 5.759 r_long_range_B_other 5.744 r_scangle_other 4.322 r_mcangle_it 2.929 r_mcangle_other 2.928 r_scbond_it 2.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.929 r_dihedral_angle_4_deg 17.695 r_dihedral_angle_3_deg 15.413 r_dihedral_angle_1_deg 5.962 r_long_range_B_refined 5.759 r_long_range_B_other 5.744 r_scangle_other 4.322 r_mcangle_it 2.929 r_mcangle_other 2.928 r_scbond_it 2.796 r_scbond_other 2.795 r_mcbond_it 1.995 r_mcbond_other 1.994 r_angle_refined_deg 1.422 r_angle_other_deg 1.307 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8949 Nucleic Acid Atoms Solvent Atoms 555 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Xia2 DIALS data scaling PHASER phasing