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Structure of the Human mitochondrial kinase COQ8A R611K with AMPPNP (Cerebellar Ataxia and Ubiquinone Deficiency Through Loss of Unorthodox Kinase Activity)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 One part of ADCK3 R611K, 0.2 mM, AMPPNP 2 mM, MgCl2, 4mM, mixed with an equal volume of sodium polyacrylate 5100, 26%; magnesium chloride, 20 mM; HEPES, 100 mM, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 150.05 α = 90 b = 59.12 β = 97.69 c = 51 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-300 2014-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.96862 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.3 50 100 0.087 0.998 12.5 7.37 19840
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 100 1.232 1.65 7.61
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.3 44.67 18275 1556 99.96 0.18952 0.18346 0.1974 0.25887 0.2684 RANDOM 76.273
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] 0.82 0.8 1.27 -2.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.669 r_dihedral_angle_4_deg 18.846 r_dihedral_angle_3_deg 18.309 r_long_range_B_refined 10.059 r_long_range_B_other 10.058 r_dihedral_angle_1_deg 8.208 r_scangle_other 7.77 r_mcangle_it 6.628 r_mcangle_other 6.628 r_scbond_it 5.345
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.669 r_dihedral_angle_4_deg 18.846 r_dihedral_angle_3_deg 18.309 r_long_range_B_refined 10.059 r_long_range_B_other 10.058 r_dihedral_angle_1_deg 8.208 r_scangle_other 7.77 r_mcangle_it 6.628 r_mcangle_other 6.628 r_scbond_it 5.345 r_scbond_other 5.344 r_mcbond_it 4.601 r_mcbond_other 4.598 r_angle_refined_deg 2.152 r_angle_other_deg 1.155 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3105 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing