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Crystal structure of respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to reduced 3-acetylpyridine adenine dinucleotide (without reducing agent)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished, isomorphous structure of oxidized NuoEF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 trisodium citrate, ammonium sulfate, sodium chloride, Tris, BisTris
Crystal Properties Matthews coefficient Solvent content 2.61 52.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.233 α = 90 b = 116.449 β = 90 c = 190.047 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 EIGER X 16M 2018-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.85 49.7 99.9 0.039 0.999 13.6 13.5 120438 18.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.88 99.9 0.421 0.848 2.1 13.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.85 49.695 120344 6201 99.919 0.172 0.1708 0.1822 0.2006 0.2113 27.406
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] 1.063 0.2 -1.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.804 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_other_3_deg 12.675 r_dihedral_angle_2_deg 6.766 r_lrange_it 6.231 r_dihedral_angle_1_deg 6.175 r_lrange_other 5.967 r_scangle_it 1.781 r_scangle_other 1.781 r_angle_refined_deg 1.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.804 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_other_3_deg 12.675 r_dihedral_angle_2_deg 6.766 r_lrange_it 6.231 r_dihedral_angle_1_deg 6.175 r_lrange_other 5.967 r_scangle_it 1.781 r_scangle_other 1.781 r_angle_refined_deg 1.165 r_scbond_it 1.132 r_scbond_other 1.132 r_mcangle_other 1.116 r_mcangle_it 1.115 r_mcbond_it 0.704 r_mcbond_other 0.702 r_angle_other_deg 0.404 r_symmetry_xyhbond_nbd_refined 0.302 r_symmetry_nbd_refined 0.247 r_nbd_refined 0.209 r_nbd_other 0.209 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.18 r_symmetry_metal_ion_refined 0.15 r_xyhbond_nbd_refined 0.144 r_metal_ion_refined 0.123 r_symmetry_nbtor_other 0.073 r_symmetry_xyhbond_nbd_other 0.073 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9083 Nucleic Acid Atoms Solvent Atoms 1065 Heterogen Atoms 250
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling REFMAC phasing