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Crystal structure of Trap1 bound to Si-MitoQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7EXP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 18 % PEG 3350
0.1 M Na-Malonate pH 6.3
25 mM Hexamine cobalt chloride
Crystal Properties Matthews coefficient Solvent content 2.35 47.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 178.618 α = 90 b = 96.693 β = 134.28 c = 125.05 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 PIXEL DECTRIS EIGER X 9M 2023-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.9794 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 50 99.9 0.995 24.52 6.4 47082 55.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 0.995
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.6 33.13 1.37 46909 1980 99.5 0.1875 0.1858 0.1912 0.226 0.2265
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 f_dihedral_angle_d 19.783 f_angle_d 0.659 f_chiral_restr 0.041 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9531 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing