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crystal structure of Acyl-CoA dehydrogenase from Thermobifida fusca
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PFD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Ammonium sulfate
Sodium citrate
Potassium sodium tartrate tetrahydrate
Crystal Properties Matthews coefficient Solvent content 4.66 73.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.721 α = 90 b = 101.721 β = 90 c = 311.936 γ = 90
Symmetry Space Group I 41 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD ADSC QUANTUM 270 2022-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97934 PAL/PLS 7A (6B, 6C1)
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 1.9 50 98.8 0.076 0.08 0.024 0.995 11.1 9.2 64134
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 1.9 1.93 98.6 0.347 0.377 0.143 0.805 5.9
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 1.9 33.73 60908 3221 98.83 0.18024 0.17938 0.1932 0.19624 0.2064 RANDOM 26.792
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] 1.43 1.43 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.371 r_dihedral_angle_4_deg 21.879 r_dihedral_angle_3_deg 14.66 r_long_range_B_refined 6.721 r_long_range_B_other 6.68 r_scangle_other 6.146 r_dihedral_angle_1_deg 5.918 r_scbond_other 4.161 r_scbond_it 4.158 r_mcangle_it 2.926
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.371 r_dihedral_angle_4_deg 21.879 r_dihedral_angle_3_deg 14.66 r_long_range_B_refined 6.721 r_long_range_B_other 6.68 r_scangle_other 6.146 r_dihedral_angle_1_deg 5.918 r_scbond_other 4.161 r_scbond_it 4.158 r_mcangle_it 2.926 r_mcangle_other 2.926 r_mcbond_it 2.289 r_mcbond_other 2.283 r_angle_refined_deg 1.852 r_angle_other_deg 1.514 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 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 2932 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction MOLREP phasing