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Crystal structure of the oxidized respiratory complex I subunit NuoEF from Aquifex aeolicus, mutation V136M(NuoE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other An unpublished structure of NuoEF_V90P_V136M was used as search model
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, 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.61 52.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.22 α = 90 b = 67.413 β = 104.839 c = 121.931 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 2018-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 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 2.05 45.62 97.8 0.059 0.997 10.2 7.1 85028
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 2.05 2.09 0.403 0.798 2.2
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 2.05 45.62 85010 4359 97.583 0.224 0.2226 0.2292 0.2581 0.2663 Random selection 26.665
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] 0.311 -0.629 0.346 -0.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.657 r_dihedral_angle_3_deg 13.338 r_dihedral_angle_other_3_deg 12.132 r_dihedral_angle_2_deg 6.197 r_dihedral_angle_1_deg 5.895 r_lrange_it 2.716 r_lrange_other 2.578 r_angle_refined_deg 1.08 r_scangle_it 0.796 r_scangle_other 0.785
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.657 r_dihedral_angle_3_deg 13.338 r_dihedral_angle_other_3_deg 12.132 r_dihedral_angle_2_deg 6.197 r_dihedral_angle_1_deg 5.895 r_lrange_it 2.716 r_lrange_other 2.578 r_angle_refined_deg 1.08 r_scangle_it 0.796 r_scangle_other 0.785 r_mcangle_it 0.653 r_mcangle_other 0.653 r_scbond_it 0.609 r_scbond_other 0.604 r_angle_other_deg 0.382 r_mcbond_it 0.375 r_mcbond_other 0.375 r_nbd_refined 0.201 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.179 r_nbd_other 0.157 r_symmetry_nbd_refined 0.149 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.095 r_symmetry_nbtor_other 0.073 r_metal_ion_refined 0.063 r_chiral_restr 0.055 r_chiral_restr_other 0.011 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9088 Nucleic Acid Atoms Solvent Atoms 694 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing