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Crystal structure of reduced 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Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously obtained, unpublished and isomorphous structure of oxidized NuoEF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 2.62 53.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.527 α = 90 b = 116.619 β = 90 c = 190.01 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 1.96 48.153 100 0.043 0.999 14.4 13.2 102156 18.86
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 1.96 1.99 100 0.318 0.864 2.6 13.4
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.96 48.153 101256 5246 99.166 0.194 0.1919 0.2244 0.2005 25.256
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] -0.583 1.355 -0.772
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.795 r_dihedral_angle_3_deg 13.62 r_dihedral_angle_other_3_deg 11.35 r_dihedral_angle_2_deg 7.223 r_dihedral_angle_1_deg 6.208 r_lrange_it 5.711 r_lrange_other 5.547 r_scangle_it 1.573 r_scangle_other 1.477 r_angle_refined_deg 1.152
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.795 r_dihedral_angle_3_deg 13.62 r_dihedral_angle_other_3_deg 11.35 r_dihedral_angle_2_deg 7.223 r_dihedral_angle_1_deg 6.208 r_lrange_it 5.711 r_lrange_other 5.547 r_scangle_it 1.573 r_scangle_other 1.477 r_angle_refined_deg 1.152 r_mcangle_it 1.108 r_mcangle_other 1.108 r_scbond_it 0.972 r_scbond_other 0.891 r_mcbond_it 0.666 r_mcbond_other 0.665 r_angle_other_deg 0.4 r_symmetry_xyhbond_nbd_other 0.244 r_symmetry_xyhbond_nbd_refined 0.235 r_nbd_refined 0.215 r_symmetry_nbd_refined 0.192 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.154 r_nbd_other 0.146 r_xyhbond_nbd_other 0.137 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 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9084 Nucleic Acid Atoms Solvent Atoms 872 Heterogen Atoms 214
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling REFMAC phasing