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Homotrimer for the lumenal domain of Vacuolar Sorting Receptor 1 (VSR1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277.15 0.1 M Tris pH 8.0, 20% v/v glycerol ethoxylate, 10% v/v tetrahydrofuran
Crystal Properties Matthews coefficient Solvent content 3.93 68.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.477 α = 90 b = 141.477 β = 90 c = 141.477 γ = 90
Symmetry Space Group P 21 3
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 PILATUS3 6M 2019-07-18 M SINGLE WAVELENGTH 2 1 x-ray 100 PIXEL DECTRIS PILATUS 12M 2024-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9796 Diamond I03 2 SYNCHROTRON DIAMOND BEAMLINE I23 3.024 Diamond I23
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 3.51 49.96 99.7 0.999 30.14 16 12055 137.53
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 3.51 3.72 98.8 0.301 28.8
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 AB INITIO PHASING FREE R-VALUE 3.51 47.16 1.34 12032 602 99.61 0.2566 0.2558 0.2555 0.2723 0.2732 133.92
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 10.5499 f_angle_d 0.4885 f_chiral_restr 0.0416 f_plane_restr 0.0037 f_bond_d 0.0026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3365 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 89
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling Arcimboldo phasing Coot model building PHASER phasing xia2 data reduction Aimless data scaling