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N-terminal of Sialoadhesin in complex with Me-a-9-N-benzoyl-amino-9-deoxy-Neu5Ac (BENZ 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 4.6 1+1 DROP WITH 22.5 % (W/V) PEG 4000, 10 MM DTT, 0.18M AMMONIUM SULFATE, 0.09M SODIUM ACETATE PH 4.6,25MM BENZ COMPOUND
Crystal Properties Matthews coefficient Solvent content 2.54 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.86 α = 90 b = 67.86 β = 90 c = 69.247 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 ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 2.1 20 99.9 0.11 23.4 11.8 9849 -1.5 18.1
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 2.1 2.17 99.8 0.72 2.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT DOMAIN A OF PDB ENTRY 1QFO 2.1 19.72 9667 512 98.3 0.209 0.209 0.253 RANDOM 39.1
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] -2.64 -2.64 5.29
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_scangle_it 6.82 c_scbond_it 5.8 c_mcangle_it 4.3 c_mcbond_it 3.58 c_angle_deg 1.3 c_improper_angle_d 0.85 c_bond_d 0.011 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.5 c_scangle_it 6.82 c_scbond_it 5.8 c_mcangle_it 4.3 c_mcbond_it 3.58 c_angle_deg 1.3 c_improper_angle_d 0.85 c_bond_d 0.011 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 71 Heterogen Atoms 35
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing