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Crystal Structure of reduced NuoEF variant E222K(NuoF) from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9FII Rfree flags were transferred from scaled data of isomorphous crystal structure 9FII followed by direct Fourier synthesis using 9FII as starting model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 281 0.1 M Tris pH 7.1, 0.85 M Na3-citrate, 0.1 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.56 51.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.984 α = 90 b = 113.438 β = 90 c = 189.11 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 2.35 48.687 99.9 0.077 0.996 7.4 6.4 58277
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 2.35 2.41 0.436 0.857
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 2.35 48.687 58200 2853 99.916 0.195 0.1931 0.2012 0.2363 0.2417 Rfree flags were transferred from scaled data of isomorphous structure (pdb ID 9FII) 36.69
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] 0.901 1.474 -2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.146 r_dihedral_angle_other_3_deg 12.631 r_dihedral_angle_6_deg 12.598 r_dihedral_angle_1_deg 5.861 r_dihedral_angle_2_deg 5.787 r_lrange_it 4.485 r_lrange_other 4.448 r_scangle_it 2.399 r_scangle_other 2.382 r_mcangle_other 1.753
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.146 r_dihedral_angle_other_3_deg 12.631 r_dihedral_angle_6_deg 12.598 r_dihedral_angle_1_deg 5.861 r_dihedral_angle_2_deg 5.787 r_lrange_it 4.485 r_lrange_other 4.448 r_scangle_it 2.399 r_scangle_other 2.382 r_mcangle_other 1.753 r_mcangle_it 1.752 r_scbond_it 1.444 r_scbond_other 1.415 r_angle_refined_deg 1.296 r_mcbond_it 1.055 r_mcbond_other 1.054 r_angle_other_deg 0.462 r_symmetry_nbd_refined 0.274 r_nbd_other 0.226 r_nbd_refined 0.204 r_symmetry_nbd_other 0.193 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.086 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.066 r_symmetry_xyhbond_nbd_other 0.054 r_bond_refined_d 0.005 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 9040 Nucleic Acid Atoms Solvent Atoms 403 Heterogen Atoms 130
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing