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A lid blocking mechanism of a cone snail toxin revealed at the atomic level
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YHT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 0.1M Sodium Chloride
9.1M Sodium Formate
0.1M Bis-Tris propane
25% PEG Smear Medium
Crystal Properties Matthews coefficient Solvent content 2.1 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.855 α = 90 b = 90.327 β = 105.28 c = 44.645 γ = 90
Symmetry Space Group P 1 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2020-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5417
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 1.798 42.31 97.21 0.0495 0.996 10.01 7.6 30334
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 1.798 1.863 0.2314 0.815
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 6YHT 1.798 42.306 1.36 30299 1506 97.22 0.184 0.1822 0.1819 0.2185 0.2175 15.4407
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2795 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHASER phasing