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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 1O7S PDB ENTRY 1O7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 0.2 M SODIUM ACETATE TRIHYDRATE 0.1 M SODIUM CACODYLATE PH 6.5, 30 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 1.731 27.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.049 α = 90 b = 40.049 β = 90 c = 140.769 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 100 CCD ADSC CCD 2001-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.9 25 94.8 0.061 11.7 3.4 9146 17.3
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 1.9 1.97 96.3 0.312 2.4 2.9
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 1O7S 1.9 24.25 9146 479 94.5 0.21 0.21 0.2115 0.258 0.2146 RANDOM 34.09
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] 2.79 2.79 -5.58
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.51 c_mcangle_it 2.796 c_scbond_it 2.297 c_mcbond_it 1.697 c_angle_deg 1.28 c_bond_d 0.01 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 3.51 c_mcangle_it 2.796 c_scbond_it 2.297 c_mcbond_it 1.697 c_angle_deg 1.28 c_bond_d 0.01 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 1029 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 83
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing