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Crystal structure of Tetraspanin TSPAN10mutant Large Extracellular Loop (LEL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9H1Z9-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.3M Diethylene glycol; 0.3M Triethylene glycol; 0.3M Tetraethylene
glycol;0.3M Pentaethylene glycol; 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.3 α = 90 b = 62.3 β = 90 c = 117.48 γ = 90
Symmetry Space Group P 43 21 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 16M 2024-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.984002 SOLEIL PROXIMA 1
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 1.55 44.05 99.91 0.999 16.22 10.29 34211 29.61
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 1.552 1.608 0.671 1.18
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 1.55 44.05 1.35 34209 1710 99.92 0.1986 0.1971 0.1972 0.2276 0.2276 37.56
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 16.4645 f_angle_d 0.8348 f_chiral_restr 0.0495 f_plane_restr 0.0088 f_bond_d 0.0059
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1772 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing Coot model building