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C-type carbohydrate-recognition domain 4 of the mannose receptor complexed with Methyl-GlcNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7JUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Protein solution: 3mg/ml protein in 5 mM CaCl2, 10 mM Tris, pH 8.0, 25 mM NaCl, and 50mM alpha-Me-GlcNAc. Reservoir solution: 20% Peg 8K, 0.1M MES, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.02 39.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.484 α = 90 b = 66.633 β = 90 c = 34.436 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 2020-09-12 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 Merge I (Observed) Rrim I (All) 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 1.75 34.44 99.7 0.072 0.075 0.021 0.998 20.2 13.2 13185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 98.2 0.384 0.399 0.108 0.979 13.3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7JUB 1.75 34.44 13153 658 99.55 0.1902 0.1886 0.1934 0.2204 0.2249 31.5273
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 1011 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 17
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHENIX refinement PDB_EXTRACT data extraction