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High resolution structure of Siglec-7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFO PDB ENTRY 1QFO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 0.2 M SODIUM ACETATE TRIHYDRATE 0.1 M TRI-SODIUM CACODYLATE, PH 6.5, 30 % PEG 8,000
Crystal Properties Matthews coefficient Solvent content 2.026 38.145
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.078 α = 90 b = 53.078 β = 90 c = 93.77 γ = 90
Symmetry Space Group P 41 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 100 CCD ADSC CCD 2001-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.75 30 100 0.065 8.6 6.1 14144 19.1
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 1.75 1.81 100 0.562 3.4 6.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1QFO 1.75 30 86594 544 100 0.221 0.221 0.2208 0.248 0.2177 RANDOM 29.3
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_scangle_it 3.142 c_mcangle_it 2.485 c_scbond_it 2.087 c_angle_deg 1.56 c_mcbond_it 1.54 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.142 c_mcangle_it 2.485 c_scbond_it 2.087 c_angle_deg 1.56 c_mcbond_it 1.54 c_bond_d 0.013 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 895 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 36
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing