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Crystal Structure of reduced NuoEF variant R66G(NuoF) from Aquifex aeolicus bound to NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FDJ Rfraa flags were transferred from the scaled data of the isomorphous structure 9FDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 281 100 mM BisTris pH 6.3, 1.4 M ammonium sulfate, 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.63 53.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.527 α = 90 b = 116.5 β = 90 c = 190.823 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 PILATUS3 6M 2021-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
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 2.2 48.2 99.9 0.07 0.996 7.9 9.7 72750
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 2.25 0.42 0.806
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 FOURIER SYNTHESIS FREE R-VALUE 2.2 48.197 72673 3621 99.816 0.188 0.1859 0.1945 0.2286 0.2355 Rfree flags were transferred from scaled data of isomorphous structure 9FDJ 29.152
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] -1.408 2.553 -1.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.69 r_dihedral_angle_other_3_deg 12.306 r_dihedral_angle_3_deg 12.28 r_dihedral_angle_2_deg 6.382 r_dihedral_angle_1_deg 6.304 r_lrange_it 4.442 r_lrange_other 4.353 r_scangle_it 1.421 r_scangle_other 1.304 r_angle_refined_deg 1.284
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.69 r_dihedral_angle_other_3_deg 12.306 r_dihedral_angle_3_deg 12.28 r_dihedral_angle_2_deg 6.382 r_dihedral_angle_1_deg 6.304 r_lrange_it 4.442 r_lrange_other 4.353 r_scangle_it 1.421 r_scangle_other 1.304 r_angle_refined_deg 1.284 r_mcangle_it 0.896 r_mcangle_other 0.896 r_scbond_it 0.866 r_scbond_other 0.762 r_mcbond_it 0.533 r_mcbond_other 0.533 r_angle_other_deg 0.442 r_symmetry_nbd_refined 0.25 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.196 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.182 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.12 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.064 r_symmetry_xyhbond_nbd_other 0.008 r_bond_refined_d 0.004 r_dihedral_angle_other_2_deg 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 9068 Nucleic Acid Atoms Solvent Atoms 673 Heterogen Atoms 252
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing