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Crystal Structure of Two N-terminal Domains of Native Siglec-5 in Complex with 3'-Sialyllactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZG2 PDB ENTRY 2ZG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 20% MPEG 550, 0.1M TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.66 66.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.134 α = 90 b = 93.134 β = 90 c = 213.558 γ = 120
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 MARMOSAIC 300 mm CCD 2006-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 3 50 99.8 0.046 34.3 7.3 7405 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 98.8 0.36 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 PDB ENTRY 2ZG2 3 25 7396 7310 485 98.8 0.236 0.2334 0.274 0.2698 random 109
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 c_mcangle_it 3.083 c_scangle_it 3.004 c_scbond_it 1.786 c_mcbond_it 1.692 c_angle_deg 1.36 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_mcangle_it 3.083 c_scangle_it 3.004 c_scbond_it 1.786 c_mcbond_it 1.692 c_angle_deg 1.36 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 43
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling