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Crystal Structure of NuoEF variant R66G(NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions after 10 min soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FDJ RFree flags were transferred from the scaled data of the previously solved structure 9FDJ, followed by direct Fourier synthesis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 281 100 mM BisTris pH 6.5, 1.4 M ammonium sulfate, 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.184 α = 90 b = 116.158 β = 90 c = 189.651 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 6M 2020-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
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 2.1 47.948 99.8 0.064 0.996 8.5 6 82223
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 2.1 2.14 0.476 0.776 1.9
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 2.1 47.948 80830 4065 98.158 0.182 0.1803 0.1892 0.22 0.2275 Rfree flags were transferred from scaled data of previously solved structure 9FDJ 32.922
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] -0.921 1.74 -0.818
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.579 r_dihedral_angle_other_3_deg 13.547 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 6.186 r_dihedral_angle_2_deg 5.759 r_lrange_it 5.209 r_lrange_other 5.118 r_scangle_it 1.754 r_scangle_other 1.668 r_mcangle_it 1.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.579 r_dihedral_angle_other_3_deg 13.547 r_dihedral_angle_3_deg 11.651 r_dihedral_angle_1_deg 6.186 r_dihedral_angle_2_deg 5.759 r_lrange_it 5.209 r_lrange_other 5.118 r_scangle_it 1.754 r_scangle_other 1.668 r_mcangle_it 1.219 r_mcangle_other 1.219 r_angle_refined_deg 1.2 r_scbond_it 1.051 r_scbond_other 0.994 r_mcbond_it 0.727 r_mcbond_other 0.727 r_angle_other_deg 0.423 r_nbd_refined 0.21 r_symmetry_xyhbond_nbd_refined 0.187 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.182 r_xyhbond_nbd_other 0.177 r_metal_ion_refined 0.17 r_nbd_other 0.153 r_xyhbond_nbd_refined 0.142 r_symmetry_nbd_refined 0.136 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.061 r_symmetry_xyhbond_nbd_other 0.021 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 9105 Nucleic Acid Atoms Solvent Atoms 778 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing