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Galectin-8 N-terminal domain in complex with sialyllactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YV8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 30%(v/v) PEG400, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.71 α = 90 b = 61.5 β = 90 c = 84.07 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS VII mirrors 2011-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.08 50 99.8 0.061 12.8 5.3 17578 18.5
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 2.08 2.15 100 0.327 4.7 5.3
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2YV8 2.08 22.6 17576 1743 99.6 0.212 0.1987 0.249 0.2357 RANDOM 44.1042
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] -10.57 -1.4 11.96
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 2.92 c_mcangle_it 2.33 c_scbond_it 2.07 c_mcbond_it 1.45 c_angle_deg 1.3 c_improper_angle_d 0.86 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2354 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 93
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing CNS refinement CrystalClear data reduction CrystalClear data scaling