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Structure of the immune receptor CD33 in complex with 6'-sialyllactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IHB PDB ENTRY 5IHB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295.15 2% PEG 20,000, 4% PEG MME 500, 100 MM BICINE/TRIS BASE PH 8.5, 1XMORPHEUS AMINO ACIDS. CRYSTALS SOAKED IN 20 MM 6'-SIALYLLACTOSE IN MOTHER LIQUOR FOR 10 DAYS.
Crystal Properties Matthews coefficient Solvent content 2.8 56.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.49 α = 90 b = 123.68 β = 90 c = 141.6 γ = 90
Symmetry Space Group P 21 21 21
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 2015-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.48 42.57 97.18 0.099 0.989 8.05 3.9 39754 1.34 62.56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.569 98 0.9263 1.28 4.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE PDB ENTRY 5IHB 2.48 42.57 1.34 39740 1909 97.18 0.2305 0.2294 0.2336 0.2513 0.2566 RANDOM 79.79
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 8.813 f_angle_d 0.586 f_chiral_restr 0.045 f_bond_d 0.003 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6636 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 280
Software Software Software Name Purpose PHENIX refinement xia2 data reduction XSCALE data scaling XDS data reduction PHASER phasing