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Siglec-7 in complex with GT1b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O7V PDB ENTRY 1O7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 200mM sodium acetate, 100mM sodium cacodylate, 30 % w/v PEG 8000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.021 α = 90 b = 46.021 β = 90 c = 106.474 γ = 120
Symmetry Space Group P 32 2 1
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 2004-04-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9756 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 1.85 15 98.3 0.073 25.5 3.6 11626 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 1.85 1.92 98.4 0.52 2.3 2.3 11626
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1O7V 1.85 15 11626 11045 551 99.35 0.196 0.19678 0.19505 0.238 0.23447 0.2636 RANDOM 24.459
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] -0.96 -0.48 -0.96 1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.613 r_scangle_it 2.573 r_mcangle_it 2.112 r_scbond_it 2.057 r_angle_refined_deg 1.486 r_mcbond_it 1.331 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.191 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.613 r_scangle_it 2.573 r_mcangle_it 2.112 r_scbond_it 2.057 r_angle_refined_deg 1.486 r_mcbond_it 1.331 r_symmetry_hbond_refined 0.192 r_symmetry_vdw_refined 0.191 r_nbd_refined 0.189 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 933 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing