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N-terminal of Sialoadhesin in complex with Me-a-9-N-(naphthyl-2-carbonyl)-amino-9-deoxy-Neu5Ac (NAP compound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFO DOMAIN A OF PDB ENTRY 1QFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 30 % (W/V) PEG 4000, 10 MM DTT, 0.1M SODIUM HEPES PH 5.6,25MM NAP COMPOUND
Crystal Properties Matthews coefficient Solvent content 2.54 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.866 α = 90 b = 64.866 β = 90 c = 64.051 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 25 97 0.24 8.4 9.6 3047 26.1
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 3 3.11 72.5 0.51 2.1
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT DOMAIN A OF PDB ENTRY 1QFO 3 19.54 2857 136 95.5 0.192 0.192 0.1843 0.272 0.2493 RANDOM 21.6
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] 5.1 5.1 -10.2
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 9.05 c_scbond_it 6.94 c_mcangle_it 5.7 c_mcbond_it 3.95 c_angle_deg 1.2 c_improper_angle_d 0.89 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25 c_scangle_it 9.05 c_scbond_it 6.94 c_mcangle_it 5.7 c_mcbond_it 3.95 c_angle_deg 1.2 c_improper_angle_d 0.89 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_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 928 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 33
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing