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Crystal structure of reduced respiratory Complex I subunits NuoEF from Aquifex aeolicus bound to reduced 3-acetylpyridine adenine dinucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously solved, isomorphous structure of the same protein, unpublished
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 Tris, BisTris, trisodium citrate, ammonium sulfate, NaCl
Crystal Properties Matthews coefficient Solvent content 2.6 52.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.413 α = 90 b = 116.013 β = 90 c = 189.741 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 2018-08-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 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 1.95 49.538 99.9 0.035 0.999 15.7 13.3 102689 29.08
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 1.95 1.98 0.436 0.737 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 1.95 49.538 102612 5309 99.787 0.168 0.1666 0.1778 0.2003 0.2108 33.148
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] -0.298 1.723 -1.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.436 r_dihedral_angle_3_deg 13.388 r_dihedral_angle_other_3_deg 12.23 r_dihedral_angle_2_deg 6.687 r_dihedral_angle_1_deg 6.267 r_lrange_it 5.95 r_lrange_other 5.817 r_scangle_it 1.747 r_scangle_other 1.642 r_mcangle_it 1.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.436 r_dihedral_angle_3_deg 13.388 r_dihedral_angle_other_3_deg 12.23 r_dihedral_angle_2_deg 6.687 r_dihedral_angle_1_deg 6.267 r_lrange_it 5.95 r_lrange_other 5.817 r_scangle_it 1.747 r_scangle_other 1.642 r_mcangle_it 1.218 r_mcangle_other 1.217 r_angle_refined_deg 1.137 r_scbond_it 1.104 r_scbond_other 1.025 r_mcbond_it 0.752 r_mcbond_other 0.751 r_angle_other_deg 0.401 r_symmetry_nbd_refined 0.3 r_nbd_other 0.208 r_nbd_refined 0.204 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.18 r_symmetry_xyhbond_nbd_refined 0.17 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.1 r_symmetry_xyhbond_nbd_other 0.094 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9069 Nucleic Acid Atoms Solvent Atoms 932 Heterogen Atoms 231
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling REFMAC phasing