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Endo180 (uPARAP) carbohydrate-recognition domain 2 with bound methyl fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E4K Chain A residues 380-506 and two Ca2+ ions
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289.5 Drop:
5.2 mg/ml protein
5 mM CaCl2
10 mM Tris-Cl, pH 8.0
25mM NaCl
50mM alpha-Methyl-Fucoside
Reservoir
26% polyethylene glycol 8K
0.1 M Tris-Cl, pH 8.0.
Crystal Properties Matthews coefficient Solvent content 1.89 34.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.65 α = 90 b = 66.56 β = 90 c = 37.23 γ = 90
Symmetry Space Group P 21 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 2021-12-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-1 0.97946 SSRL BL12-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.9 40 100 0.125 0.99 21.08 24.7 9435 24
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 1.9 1.97 100 0.992 22.4
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 1.9 37.65 1.38 9385 472 99.78 0.1865 0.1837 0.1839 0.2386 0.2388 32.92
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 13.464 f_angle_d 0.8054 f_chiral_restr 0.0564 f_plane_restr 0.0062 f_bond_d 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1036 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing