☰ Navigation Tabs
Crystal structure of Siglec-7 in complex with methyl-9-(aminooxalyl-amino)-9-deoxyNeu5Ac (oxamido-Neu5Ac)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7S Siglec-7, APO, 1o7S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 293 30% PEG 4000, 0.1M sodium acetate, pH 4.6, 0.2M ammonium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.928 α = 90 b = 52.928 β = 90 c = 93.236 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 QUANTUM 4 2003-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.933 ESRF ID14-4
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 1.6 25 97.5 0.043 21.5 4.2 17748 2 2
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 1.6 1.66 78.9 0.338 2 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 (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Siglec-7, APO, 1o7S 1.6 25 17691 893 97.56 0.214 0.214 0.213 0.2239 0.228 RANDOM 19.424
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] 0.56 0.56 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.027 r_scangle_it 3.311 r_mcangle_it 2.863 r_scbond_it 2.448 r_mcbond_it 1.77 r_angle_refined_deg 1.347 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.027 r_scangle_it 3.311 r_mcangle_it 2.863 r_scbond_it 2.448 r_mcbond_it 1.77 r_angle_refined_deg 1.347 r_nbd_refined 0.186 r_symmetry_vdw_refined 0.149 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 904 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing