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Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V136M(NuoE), bound to NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other An in-house model of the same protein without nucleotide (now pdb ID 9HEG) was used
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.1 M BisTris, 1.35-1.45 M ammonium sulfate, 0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.58 52.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.723 α = 90 b = 63.372 β = 107.258 c = 123.429 γ = 90
Symmetry Space Group P 1 21 1
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 6M 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 2.6 46.2 99.5 0.067 0.996 9.2 7.1 42296
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 2.6 2.7 99.7 0.447 0.8 1.8 7.2
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.6 46.2 42278 2154 99.347 0.248 0.2456 0.2518 0.2901 0.2954 Random selection 43.067
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] 0.884 -3.318 1.548 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.99 r_dihedral_angle_6_deg 13.094 r_dihedral_angle_other_3_deg 12.236 r_dihedral_angle_2_deg 5.76 r_dihedral_angle_1_deg 5.536 r_lrange_it 3.806 r_lrange_other 3.796 r_scangle_it 1.444 r_scangle_other 1.406 r_mcangle_it 1.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.99 r_dihedral_angle_6_deg 13.094 r_dihedral_angle_other_3_deg 12.236 r_dihedral_angle_2_deg 5.76 r_dihedral_angle_1_deg 5.536 r_lrange_it 3.806 r_lrange_other 3.796 r_scangle_it 1.444 r_scangle_other 1.406 r_mcangle_it 1.322 r_mcangle_other 1.322 r_angle_refined_deg 1.186 r_scbond_it 0.901 r_scbond_other 0.845 r_mcbond_it 0.779 r_mcbond_other 0.779 r_angle_other_deg 0.416 r_symmetry_xyhbond_nbd_refined 0.239 r_nbd_refined 0.2 r_symmetry_nbd_other 0.2 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.18 r_nbd_other 0.166 r_symmetry_nbd_refined 0.153 r_symmetry_xyhbond_nbd_other 0.145 r_metal_ion_refined 0.108 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.056 r_chiral_restr_other 0.015 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 9065 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 196
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing