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Crystal Structure of oxidized NuoEF variant E222K(NuoF) from Aquifex aeolicus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HL2 chains A and B were placed two times independepently in the asymmetric unit
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 2.66 53.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.072 α = 90 b = 113.397 β = 90 c = 189.555 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 2.5 48.1 97.3 0.099 0.988 5.6 3.7 47026
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 2.5 2.59 0.467 0.769
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 2.5 47.434 46977 2291 96.516 0.21 0.2076 0.2139 0.2494 0.2543 Random selection 31.479
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] 0.979 0.025 -1.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.441 r_dihedral_angle_6_deg 13.127 r_dihedral_angle_other_3_deg 13.025 r_dihedral_angle_2_deg 8.791 r_dihedral_angle_1_deg 6.118 r_lrange_it 3.995 r_lrange_other 3.968 r_scangle_it 1.595 r_scangle_other 1.595 r_angle_refined_deg 1.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.441 r_dihedral_angle_6_deg 13.127 r_dihedral_angle_other_3_deg 13.025 r_dihedral_angle_2_deg 8.791 r_dihedral_angle_1_deg 6.118 r_lrange_it 3.995 r_lrange_other 3.968 r_scangle_it 1.595 r_scangle_other 1.595 r_angle_refined_deg 1.455 r_mcangle_it 1.392 r_mcangle_other 1.392 r_scbond_it 0.921 r_scbond_other 0.921 r_mcbond_it 0.785 r_mcbond_other 0.783 r_angle_other_deg 0.496 r_nbd_other 0.236 r_nbd_refined 0.199 r_symmetry_nbd_other 0.197 r_symmetry_nbd_refined 0.192 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.068 r_metal_ion_refined 0.063 r_symmetry_xyhbond_nbd_other 0.032 r_chiral_restr_other 0.021 r_bond_refined_d 0.006 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 9072 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing