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Crystal structure of oxidized respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to ADP-ribose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other isomorphous structure from unpublished inhouse data
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 2.59 52.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.129 α = 90 b = 116.146 β = 90 c = 189.485 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 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 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 2 49.561 99.8 0.039 0.999 12.8 13.6 94748 1.5 31.47
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 2 2.03 99.9 0.567 0.777 1.6 14.2
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 2 49.561 94668 4892 99.685 0.179 0.1775 0.1876 0.2071 0.2179 35.457
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] -0.623 1.771 -1.149
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 19.781 r_dihedral_angle_6_deg 14.252 r_dihedral_angle_3_deg 12.662 r_dihedral_angle_1_deg 6.165 r_lrange_it 5.481 r_lrange_other 5.377 r_dihedral_angle_2_deg 5.298 r_scangle_it 1.652 r_scangle_other 1.605 r_mcangle_it 1.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 19.781 r_dihedral_angle_6_deg 14.252 r_dihedral_angle_3_deg 12.662 r_dihedral_angle_1_deg 6.165 r_lrange_it 5.481 r_lrange_other 5.377 r_dihedral_angle_2_deg 5.298 r_scangle_it 1.652 r_scangle_other 1.605 r_mcangle_it 1.201 r_mcangle_other 1.201 r_scbond_it 1.035 r_angle_refined_deg 1.029 r_scbond_other 0.999 r_mcbond_it 0.753 r_mcbond_other 0.752 r_angle_other_deg 0.355 r_nbd_refined 0.2 r_nbd_other 0.188 r_nbtor_refined 0.18 r_symmetry_nbd_other 0.179 r_symmetry_nbd_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.155 r_metal_ion_refined 0.139 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.053 r_symmetry_xyhbond_nbd_other 0.04 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9092 Nucleic Acid Atoms Solvent Atoms 868 Heterogen Atoms 216
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling