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Crystal Structure of reduced NuoEF variant P228R(NuoF) from Aquifex aeolicus bound to NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HL2 Chains A and B were used as ensemble that was placed two times independently in the asymmetric unit
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 281 100 mM BisTris pH 6.5, 1.6 M ammonium sulfate, 150 mM NaCl
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.582 α = 90 b = 115.785 β = 90 c = 190.011 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 1.66 49.486 97.2 0.064 0.993 6.9 4 161000
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 1.66 1.69 0.506 0.62
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 1.66 49.486 160798 7928 96.865 0.174 0.1729 0.1846 0.1963 0.2058 Random selection 22.061
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] 0.196 0.732 -0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.093 r_dihedral_angle_other_3_deg 14.795 r_dihedral_angle_3_deg 11.391 r_dihedral_angle_2_deg 7.829 r_lrange_it 6.046 r_dihedral_angle_1_deg 6.031 r_lrange_other 5.876 r_scangle_it 2.56 r_scangle_other 2.487 r_scbond_it 1.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.093 r_dihedral_angle_other_3_deg 14.795 r_dihedral_angle_3_deg 11.391 r_dihedral_angle_2_deg 7.829 r_lrange_it 6.046 r_dihedral_angle_1_deg 6.031 r_lrange_other 5.876 r_scangle_it 2.56 r_scangle_other 2.487 r_scbond_it 1.614 r_mcangle_it 1.579 r_mcangle_other 1.579 r_scbond_other 1.565 r_angle_refined_deg 1.476 r_mcbond_it 0.951 r_mcbond_other 0.95 r_angle_other_deg 0.517 r_nbd_refined 0.224 r_xyhbond_nbd_other 0.201 r_nbd_other 0.192 r_symmetry_nbd_other 0.191 r_metal_ion_refined 0.188 r_nbtor_refined 0.185 r_symmetry_nbd_refined 0.175 r_xyhbond_nbd_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_other 0.103 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9138 Nucleic Acid Atoms Solvent Atoms 1156 Heterogen Atoms 211
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing