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N-terminal of Sialoadhesin in complex with Me-a-9-N-(biphenyl-4-carbonyl)-amino-9-deoxy-Neu5Ac (BIP 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 ONE + ONE DROP WITH 30 % (W/V) PEG 4000, 10 MM DTT, 0.2M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH 5.6,2.5MM BIP COMPOUND
Crystal Properties Matthews coefficient Solvent content 2.54 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.61 α = 90 b = 66.61 β = 90 c = 66.947 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 3.3 20 89.7 0.192 9.2 5.5 2271
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 3.42 18.1 0.32 1.8
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 3.31 19.26 2154 195 87 0.217 0.217 0.284 RANDOM 35.1
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] -16 -16 32
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26 c_scangle_it 9.86 c_scbond_it 6.9 c_mcangle_it 5.86 c_mcbond_it 3.8 c_angle_deg 1.4 c_improper_angle_d 0.85 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26 c_scangle_it 9.86 c_scbond_it 6.9 c_mcangle_it 5.86 c_mcbond_it 3.8 c_angle_deg 1.4 c_improper_angle_d 0.85 c_bond_d 0.008 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 914 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 35
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing