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Crystal Structure of oxidized NuoEF variant P228R(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 used as ensemble, which was placed two times to fill the asymmetric unit
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 281 100 mM BisTris pH 6.3, 1.65 M ammonium sulfate, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.6 52.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.283 α = 90 b = 116.13 β = 90 c = 189.842 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 2.28 48.001 98 0.089 0.982 5.7 4 63251
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 2.28 2.34 0.323 0.797
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 2.28 48.001 62976 3160 97.293 0.2 0.1975 0.2053 0.2443 0.2512 Random selection 23.267
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] -1.186 2.524 -1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 15.306 r_dihedral_angle_6_deg 13.485 r_dihedral_angle_3_deg 12.908 r_dihedral_angle_2_deg 8.235 r_dihedral_angle_1_deg 6.429 r_lrange_it 3.094 r_lrange_other 2.905 r_angle_refined_deg 1.463 r_scangle_it 1.32 r_scangle_other 1.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_3_deg 15.306 r_dihedral_angle_6_deg 13.485 r_dihedral_angle_3_deg 12.908 r_dihedral_angle_2_deg 8.235 r_dihedral_angle_1_deg 6.429 r_lrange_it 3.094 r_lrange_other 2.905 r_angle_refined_deg 1.463 r_scangle_it 1.32 r_scangle_other 1.269 r_scbond_it 0.844 r_mcangle_it 0.796 r_mcangle_other 0.796 r_scbond_other 0.794 r_angle_other_deg 0.513 r_mcbond_it 0.472 r_mcbond_other 0.472 r_nbd_refined 0.217 r_symmetry_nbd_refined 0.208 r_symmetry_nbd_other 0.191 r_symmetry_xyhbond_nbd_refined 0.19 r_nbtor_refined 0.183 r_nbd_other 0.167 r_xyhbond_nbd_refined 0.163 r_metal_ion_refined 0.136 r_symmetry_xyhbond_nbd_other 0.078 r_chiral_restr 0.075 r_symmetry_nbtor_other 0.074 r_chiral_restr_other 0.018 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 9089 Nucleic Acid Atoms Solvent Atoms 726 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing