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Crystal Structure of NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NADH under anoxic conditions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HL2 Chains A and B were placed independently two times in the asymmetric unit
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 281 0.1 M BisTris pH 6.3, 1.6 M ammonium sulfate, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.69 54.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.399 α = 90 b = 116.035 β = 90 c = 189.72 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 1.77 48.037 100 0.047 0.997 9.2 6.2 136928
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 1.77 1.8 0.487 0.721
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 1.77 48.037 136826 6886 99.935 0.165 0.1633 0.1747 0.1886 0.1965 Random selection 27.176
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] 0.745 0.533 -1.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.61 r_dihedral_angle_other_3_deg 13.803 r_dihedral_angle_3_deg 11.475 r_dihedral_angle_2_deg 6.719 r_dihedral_angle_1_deg 6.051 r_lrange_it 5.335 r_lrange_other 5.105 r_scangle_it 2.822 r_scangle_other 2.771 r_scbond_it 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.61 r_dihedral_angle_other_3_deg 13.803 r_dihedral_angle_3_deg 11.475 r_dihedral_angle_2_deg 6.719 r_dihedral_angle_1_deg 6.051 r_lrange_it 5.335 r_lrange_other 5.105 r_scangle_it 2.822 r_scangle_other 2.771 r_scbond_it 1.746 r_scbond_other 1.712 r_mcangle_it 1.565 r_mcangle_other 1.565 r_angle_refined_deg 1.382 r_mcbond_it 1.009 r_mcbond_other 1.009 r_angle_other_deg 0.486 r_symmetry_nbd_refined 0.277 r_nbd_refined 0.213 r_nbd_other 0.201 r_symmetry_nbd_other 0.186 r_nbtor_refined 0.184 r_symmetry_xyhbond_nbd_refined 0.168 r_xyhbond_nbd_refined 0.152 r_symmetry_xyhbond_nbd_other 0.135 r_xyhbond_nbd_other 0.126 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.071 r_metal_ion_refined 0.049 r_bond_refined_d 0.005 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 9125 Nucleic Acid Atoms Solvent Atoms 992 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing