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Crystal Structure of oxidized 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 transferred from isomorphous data set of NuoEF_R66G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 281 0.1 M BisTris pH 6.3, 1.4 M ammonium sulfate, 100 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.6 52.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.283 α = 90 b = 116.318 β = 90 c = 189.318 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 1.8 63.3 99.9 0.042 0.998 11 6.3 130020
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 1.8 1.83 0.456 0.787 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 1.8 60.091 129899 6583 99.82 0.157 0.1558 0.1688 0.1864 0.1993 Random selection 27.098
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] 0.184 1.248 -1.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.678 r_dihedral_angle_other_3_deg 13.015 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_2_deg 6.741 r_dihedral_angle_1_deg 5.985 r_lrange_it 5.17 r_lrange_other 5.055 r_scangle_it 3.221 r_scangle_other 3.136 r_scbond_it 2.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.678 r_dihedral_angle_other_3_deg 13.015 r_dihedral_angle_3_deg 11.567 r_dihedral_angle_2_deg 6.741 r_dihedral_angle_1_deg 5.985 r_lrange_it 5.17 r_lrange_other 5.055 r_scangle_it 3.221 r_scangle_other 3.136 r_scbond_it 2.018 r_scbond_other 1.951 r_mcangle_it 1.547 r_mcangle_other 1.547 r_angle_refined_deg 1.434 r_mcbond_it 1.048 r_mcbond_other 1.045 r_angle_other_deg 0.498 r_metal_ion_refined 0.275 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.215 r_nbd_other 0.186 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.173 r_xyhbond_nbd_refined 0.147 r_xyhbond_nbd_other 0.121 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.073 r_chiral_restr_other 0.031 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 9103 Nucleic Acid Atoms Solvent Atoms 886 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing