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Energetic and structural basis of sialylated oligosaccharide recognition by the natural killer cell inhibitory receptor p75/AIRM1 or Siglec-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.2 298 PEG 4000 20%, NaCl 0.2 M, 0.1 M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.94 36.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.461 α = 90 b = 49.715 β = 113.08 c = 39.787 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 CCD ADSC QUANTUM 4 2000-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9 CHESS F1
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 1.45 15 75 19800 2 2 19.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.45 15 95.3
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 THROUGHOUT 1QFO 1.45 14.93 2 19760 830 95.3 0.277 0.277 0.2747 0.301 0.299 RANDOM 21.5
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] -3.01 -3.37 3.91 -0.9
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 28.4 c_mcangle_it 4.83 c_scangle_it 4.61 c_scbond_it 3.65 c_mcbond_it 3.49 c_angle_deg 2.2 c_improper_angle_d 1.17 c_bond_d 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 991 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing