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Structure of the Tetrapod Ancestor COQ8A in complex with AMP-PNP 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 6.5 293.15 10 mg/ml protein and 0.12 M monosaccharides mix (0.2 M D-glucose, 0.2 M D-mannose, 0.2 M D-galactose, 0.2 M L-fucose, 0.2 M D-xylose, 0.2 M N-acetyl-D-glucosamine), 0.1 M buffer system 1 pH 6.5 (0.5 M imidazole, 0.5 M MES monohydrate acid), 50% (v/v) precipitant mix 2 (40% (v/v) ethylene glycol, 20% (w/v) PEG 8000)
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.456 α = 90 b = 80.258 β = 90 c = 87.504 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 PILATUS4 XE 4M 2025-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.1 46.22 100 0.152 0.166 0.065 0.996 10.6 6.5 154277
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 1.166 1.271 0.501 0.541 6.4
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 THROUGHOUT 2.1 46.219 23900 1121 99.958 0.189 0.1858 0.1946 0.2552 0.2613 RANDOM 29.387
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] -0.643 0.787 -0.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.991 r_dihedral_angle_6_deg 14.413 r_dihedral_angle_2_deg 11.507 r_lrange_it 7.036 r_lrange_other 7.022 r_dihedral_angle_1_deg 6.233 r_scangle_it 5.833 r_scangle_other 5.832 r_scbond_it 3.799 r_scbond_other 3.799
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.991 r_dihedral_angle_6_deg 14.413 r_dihedral_angle_2_deg 11.507 r_lrange_it 7.036 r_lrange_other 7.022 r_dihedral_angle_1_deg 6.233 r_scangle_it 5.833 r_scangle_other 5.832 r_scbond_it 3.799 r_scbond_other 3.799 r_mcangle_it 3.368 r_mcangle_other 3.367 r_mcbond_it 2.384 r_mcbond_other 2.379 r_angle_refined_deg 1.812 r_angle_other_deg 0.579 r_chiral_restr_other 0.271 r_nbd_refined 0.233 r_nbd_other 0.225 r_symmetry_nbd_other 0.198 r_symmetry_nbd_refined 0.195 r_nbtor_refined 0.186 r_symmetry_xyhbond_nbd_refined 0.184 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.082 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.041 r_dihedral_angle_other_2_deg 0.019 r_bond_refined_d 0.008 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 3151 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction XDS data reduction