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Structural basis of glycan specificity and identification of a novel glycan binding cavity in human P[19] rotavirus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GJ6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% w/v polyethylene glycol MME 5000
Crystal Properties Matthews coefficient Solvent content 3.09 60.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.776 α = 90 b = 129.346 β = 116.07 c = 86.365 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 123 CCD ADSC QUANTUM 315r 2017-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97915 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.1 50 99.9 10.575 6.3 104019
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 6.4
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 FREE R-VALUE 5GJ6 2.1 49.675 98627 4951 94.06 0.1827 0.1812 0.1823 0.213 0.2127 31.9
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 10256 Nucleic Acid Atoms Solvent Atoms 982 Heterogen Atoms 164
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing