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crystal structure of acyl-CoA dehydrogenase FadE2 mutant (PA0508 M130G E296A Q303A) from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8PNG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 25% (w/v) PEG 1500 ; 0.1 M PCB (pH 7.0)
Crystal Properties Matthews coefficient Solvent content 2.26 45.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.892 α = 90 b = 64.756 β = 90 c = 287.954 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 XE 16M 2023-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
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 1.62 71.99 99.76 0.144 0.15 0.042 0.998 9.7 12.3 147729
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 1.62 1.65 94.93 2.632 2.884 1.143 0.31 0.3 6
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 8PNG 1.62 71.99 144075 2005 98.64 0.19181 0.19135 0.2049 0.22358 0.2341 RANDOM 28.605
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] -1.14 3.51 -2.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 13.777 r_dihedral_angle_1_deg 5.935 r_long_range_B_refined 5.494 r_long_range_B_other 5.424 r_scangle_other 4.414 r_scbond_it 2.928 r_scbond_other 2.928 r_mcangle_it 2.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.176 r_dihedral_angle_4_deg 18.792 r_dihedral_angle_3_deg 13.777 r_dihedral_angle_1_deg 5.935 r_long_range_B_refined 5.494 r_long_range_B_other 5.424 r_scangle_other 4.414 r_scbond_it 2.928 r_scbond_other 2.928 r_mcangle_it 2.551 r_mcangle_other 2.551 r_mcbond_it 1.892 r_mcbond_other 1.892 r_angle_refined_deg 1.479 r_angle_other_deg 1.416 r_chiral_restr 0.075 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 8930 Nucleic Acid Atoms Solvent Atoms 852 Heterogen Atoms 134
Software Software Software Name Purpose REFMAC refinement DIALS data scaling xia2 data reduction PHASER phasing