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Structure of the Tetrapod Ancestor COQ8B in complex with ADP and 2Mn(II)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 15 mg/ml protein and 0.09 M halogens mix (0.3 M sodium fluoride, 0.3 M sodium bromide, 0.3 M sodium iodide), 0.1 M buffer system 2 pH 7.5 (0.5 M sodium Hepes, 0.5 M bicine), 50% (v/v) precipitant mix 4 (25% (v/v) MPD, 25% (w/v) PEG 1000, 25% (w/v) PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.488 α = 90 b = 150.488 β = 90 c = 150.488 γ = 90
Symmetry Space Group P 41 3 2
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 EIGER X 9M 2025-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731281579802835 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.398 106.411 100 0.144 0.996 8.3 6.6 23456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 1.153 0.615
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.398 106.411 23397 1180 99.898 0.187 0.1844 0.1921 0.2374 0.2472 51.862
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.53 r_dihedral_angle_6_deg 15.128 r_lrange_it 12.736 r_lrange_other 12.691 r_scangle_it 10.081 r_scangle_other 10.079 r_mcangle_it 7.958 r_mcangle_other 7.955 r_dihedral_angle_2_deg 7.669 r_dihedral_angle_1_deg 7.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.53 r_dihedral_angle_6_deg 15.128 r_lrange_it 12.736 r_lrange_other 12.691 r_scangle_it 10.081 r_scangle_other 10.079 r_mcangle_it 7.958 r_mcangle_other 7.955 r_dihedral_angle_2_deg 7.669 r_dihedral_angle_1_deg 7.318 r_scbond_it 6.65 r_scbond_other 6.649 r_mcbond_it 5.535 r_mcbond_other 5.459 r_angle_refined_deg 1.918 r_angle_other_deg 0.656 r_symmetry_xyhbond_nbd_other 0.458 r_symmetry_nbd_refined 0.265 r_nbd_refined 0.23 r_symmetry_nbd_other 0.196 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.185 r_nbd_other 0.172 r_metal_ion_refined 0.119 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.08 r_bond_refined_d 0.008 r_dihedral_angle_other_2_deg 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2968 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement MOLREP phasing Aimless data scaling xia2 data reduction