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Wnt binding to COPalpha and COPBeta2 directs secretion on extracellular vesicles
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YNN 2YNN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 291 0.1M Hepes 7.0
2.0M AmSO4
Crystal Properties Matthews coefficient Solvent content 4.04 69.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 160.457 α = 107.268 b = 160.656 β = 107.157 c = 160.619 γ = 107.241
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 PILATUS 6M 2021-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.979335 ALBA XALOC
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 1.808 139.2 95.5 0.99 8.53 3.5 1088963
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 1.81 1.92 0.31
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2YNN 1.808 49.377 879297 44507 72.385 0.16 0.1594 0.1953 0.1744 0.2111 29.659
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] -0.112 -7.736 -11.265 -2.889 8.738 3.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.728 r_dihedral_angle_4_deg 15.84 r_dihedral_angle_3_deg 15.281 r_dihedral_angle_1_deg 8.121 r_lrange_it 2.821 r_lrange_other 2.669 r_mcangle_it 1.256 r_mcangle_other 1.256 r_angle_refined_deg 1.247 r_angle_other_deg 1.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.728 r_dihedral_angle_4_deg 15.84 r_dihedral_angle_3_deg 15.281 r_dihedral_angle_1_deg 8.121 r_lrange_it 2.821 r_lrange_other 2.669 r_mcangle_it 1.256 r_mcangle_other 1.256 r_angle_refined_deg 1.247 r_angle_other_deg 1.041 r_scangle_it 0.788 r_scangle_other 0.788 r_mcbond_it 0.729 r_mcbond_other 0.729 r_scbond_it 0.478 r_scbond_other 0.478 r_nbd_refined 0.171 r_symmetry_nbd_other 0.171 r_nbd_other 0.159 r_nbtor_refined 0.157 r_symmetry_xyhbond_nbd_refined 0.136 r_xyhbond_nbd_refined 0.125 r_symmetry_nbd_refined 0.122 r_symmetry_nbtor_other 0.067 r_chiral_restr 0.042 r_symmetry_xyhbond_nbd_other 0.034 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 59524 Nucleic Acid Atoms Solvent Atoms 3348 Heterogen Atoms 1372
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing