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Crystal Structure of reduced NuoEF variant R66G(NuoF) from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FDJ Rfree flags were transferred from a previously solved isomorphous structure (PDB ID 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 2.69 54.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.303 α = 90 b = 116.215 β = 90 c = 189.543 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 1.986 49.587 99.4 0.066 0.994 8 4.6 96723
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 1.986 2.02 0.381 0.807
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 1.986 49.587 96632 4847 99.284 0.167 0.1648 0.1782 0.2013 0.2113 Transfer from scaled data of PDB-ID 9FDJ 27.952
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] 0.14 1.723 -1.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.399 r_dihedral_angle_other_3_deg 12.556 r_dihedral_angle_3_deg 11.837 r_dihedral_angle_2_deg 7.067 r_dihedral_angle_1_deg 6.055 r_lrange_it 5.796 r_lrange_other 5.624 r_scangle_it 2.421 r_scangle_other 2.338 r_scbond_it 1.511
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.399 r_dihedral_angle_other_3_deg 12.556 r_dihedral_angle_3_deg 11.837 r_dihedral_angle_2_deg 7.067 r_dihedral_angle_1_deg 6.055 r_lrange_it 5.796 r_lrange_other 5.624 r_scangle_it 2.421 r_scangle_other 2.338 r_scbond_it 1.511 r_scbond_other 1.438 r_angle_refined_deg 1.403 r_mcangle_it 1.39 r_mcangle_other 1.39 r_mcbond_it 0.875 r_mcbond_other 0.874 r_angle_other_deg 0.476 r_metal_ion_refined 0.227 r_nbd_refined 0.217 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.186 r_nbtor_refined 0.182 r_xyhbond_nbd_refined 0.171 r_nbd_other 0.167 r_symmetry_nbd_refined 0.141 r_xyhbond_nbd_other 0.097 r_symmetry_xyhbond_nbd_other 0.081 r_symmetry_nbtor_other 0.074 r_symmetry_metal_ion_refined 0.071 r_chiral_restr 0.068 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 9100 Nucleic Acid Atoms Solvent Atoms 849 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing