☰ Navigation Tabs
Crystal structure of the Acyl-CoA dehydrogenase FadE1(PA0506) E441A from Pseudomonas aeruginosa complexed with C16CoA
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 6.5 298 0.1M Bis Tris Propane pH 6.5, 0.2M sodium nitrate, 20% w/v PEG 3350, 10% v/v ethylene glycol, 5mM C16CoA
Crystal Properties Matthews coefficient Solvent content 2.45 49.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.955 α = 90 b = 92.955 β = 90 c = 128.782 γ = 120
Symmetry Space Group P 31 1 2
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 XE 9M 2021-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.44 128.78 100 0.194 0.197 0.031 0.999 11.5 38.5 114956 15.1
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 1.44 1.46 100 4.451 4.529 0.834 0.3 0.4 29.3
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 1.44 80.63 109044 5767 99.92 0.1861 0.18462 0.1943 0.21378 0.2176 RANDOM 22.81
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] -0.32 -0.16 -0.32 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.731 r_dihedral_angle_4_deg 18.008 r_dihedral_angle_3_deg 13.711 r_dihedral_angle_1_deg 5.931 r_long_range_B_refined 5.706 r_long_range_B_other 5.596 r_scangle_other 4.449 r_scbond_it 3.004 r_scbond_other 3.003 r_mcangle_it 2.289
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.731 r_dihedral_angle_4_deg 18.008 r_dihedral_angle_3_deg 13.711 r_dihedral_angle_1_deg 5.931 r_long_range_B_refined 5.706 r_long_range_B_other 5.596 r_scangle_other 4.449 r_scbond_it 3.004 r_scbond_other 3.003 r_mcangle_it 2.289 r_mcangle_other 2.289 r_mcbond_it 1.632 r_mcbond_other 1.631 r_angle_refined_deg 1.629 r_angle_other_deg 1.506 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 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 4563 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement PHASER phasing xia2 data scaling xia2 data reduction