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Crystal structure of the NuoEF variant R66G (NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions (short soak)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HL2
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 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.241 α = 90 b = 116.156 β = 90 c = 189.026 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 1.7 47.932 99.9 0.034 0.999 11.6 5.8 153510
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 1.7 1.73 0.427 0.787 1.6
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 1.7 47.932 153402 7788 99.901 0.159 0.1581 0.1704 0.184 0.1955 Random selection 28.128
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] 0.883 0.813 -1.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.206 r_dihedral_angle_other_3_deg 13.307 r_dihedral_angle_3_deg 11.607 r_dihedral_angle_2_deg 6.652 r_dihedral_angle_1_deg 6.012 r_lrange_it 5.588 r_lrange_other 5.421 r_scangle_it 3.322 r_scangle_other 3.249 r_scbond_it 2.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.206 r_dihedral_angle_other_3_deg 13.307 r_dihedral_angle_3_deg 11.607 r_dihedral_angle_2_deg 6.652 r_dihedral_angle_1_deg 6.012 r_lrange_it 5.588 r_lrange_other 5.421 r_scangle_it 3.322 r_scangle_other 3.249 r_scbond_it 2.108 r_scbond_other 2.051 r_mcangle_it 1.714 r_mcangle_other 1.713 r_angle_refined_deg 1.482 r_mcbond_it 1.151 r_mcbond_other 1.146 r_angle_other_deg 0.515 r_nbd_refined 0.22 r_symmetry_nbd_other 0.187 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.184 r_nbd_other 0.166 r_metal_ion_refined 0.165 r_xyhbond_nbd_refined 0.141 r_xyhbond_nbd_other 0.118 r_symmetry_nbd_refined 0.089 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.075 r_chiral_restr_other 0.026 r_symmetry_xyhbond_nbd_other 0.025 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9081 Nucleic Acid Atoms Solvent Atoms 882 Heterogen Atoms 205
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing