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Crystal structure of the N-terminal domain of Siglec-8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2N7A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1 M Bis-Tris HCl pH 6.5, and 27% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.075 α = 90 b = 36.365 β = 90.05 c = 167.516 γ = 90
Symmetry Space Group P 1 21 1
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 2020-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97918 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.34 83.82 99.8 0.179 0.075 0.99 10.8 6.7 36480 34.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.34 2.42 99.6 1.249 0.526 0.63 2.6 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 THROUGHOUT 2N7A 2.34 83.758 1.33 36474 1913 99.78 0.2087 0.2061 0.2056 0.2565 0.2562 39.4992
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 6727 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction PDB_EXTRACT data extraction autoPROC data scaling PHASER phasing