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Crystal structure of oxidized respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to oxidized 3-acetylpyridine adenine dinucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously obtained, unpublished and isomorphous structure of oxidized NuoEF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 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.537 α = 90 b = 116.328 β = 90 c = 189.621 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 PILATUS 2M-F 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9116 SLS X06DA
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 1.6 49.627 100 0.033 0.999 14.3 13.4 185561 15.97
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 1.6 1.63 100 0.429 0.729 1.8 13.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.6 49.627 185449 9369 99.959 0.163 0.1618 0.1737 0.1872 0.198 21.269
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] 0.013 0.552 -0.565
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.345 r_dihedral_angle_3_deg 12.766 r_dihedral_angle_other_3_deg 12.542 r_dihedral_angle_2_deg 7.633 r_dihedral_angle_1_deg 6.149 r_lrange_it 5.746 r_lrange_other 5.523 r_scangle_it 2.517 r_scangle_other 2.456 r_scbond_it 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.345 r_dihedral_angle_3_deg 12.766 r_dihedral_angle_other_3_deg 12.542 r_dihedral_angle_2_deg 7.633 r_dihedral_angle_1_deg 6.149 r_lrange_it 5.746 r_lrange_other 5.523 r_scangle_it 2.517 r_scangle_other 2.456 r_scbond_it 1.63 r_scbond_other 1.586 r_angle_refined_deg 1.407 r_mcangle_it 1.367 r_mcangle_other 1.367 r_mcbond_it 0.889 r_mcbond_other 0.889 r_angle_other_deg 0.492 r_symmetry_nbd_refined 0.256 r_nbd_refined 0.224 r_symmetry_xyhbond_nbd_other 0.212 r_nbd_other 0.197 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.124 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9073 Nucleic Acid Atoms Solvent Atoms 1209 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling REFMAC phasing