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Crystal structure of basic winged bean lectin in complex with B blood group disaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.05 298 6-7% (w/v) PEG 4000 and 5% (v/v) Isopropenol, pH 7.05, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.367 α = 90 b = 91.093 β = 90 c = 73.399 γ = 90
Symmetry Space Group P 21 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 298 IMAGE PLATE MAR scanner 345 mm plate M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5481
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 2.4 30 96.3 0.096 12.3 40489 27.3
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 2.4 2.49 89 0.411 3.3
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION THROUGHOUT 1wbl 2.4 29.93 40450 1625 96.2 0.202 0.202 0.214 0.24 0.242 RANDOM 39.2
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] -8.68 17.77 -9.08
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 3.17 c_mcangle_it 2.2 c_scbond_it 2.1 c_angle_deg 1.5 c_mcbond_it 1.28 c_improper_angle_d 0.96 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7313 Nucleic Acid Atoms Solvent Atoms 338 Heterogen Atoms 449
Software Software Software Name Purpose CNS refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling CNS phasing