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Crystal structure of basic winged bean lectin in complex with b blood group trisaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WBL PDB RNTRY 1WBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.05 293 6-7%(w/v) PEG 6000, 10%(v/v) isopropenol, 20mM PBS, pH 7.05, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 50.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.41 α = 90 b = 90.545 β = 90 c = 73.324 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 293 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 1.548
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 2.75 30 96.9 0.131 12.7 3.3 27614 64.9
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 2.75 2.85 92.5 0.5 2.1 2.1
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 RNTRY 1WBL 2.75 29.74 27152 1061 97.1 0.198 0.198 0.1897 0.258 0.2501 RANDOM 32.7
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] -5.57 15.35 -9.77
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_scangle_it 2.73 c_mcangle_it 1.99 c_scbond_it 1.74 c_angle_deg 1.5 c_mcbond_it 1.16 c_improper_angle_d 1.06 c_bond_d 0.008 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.3 c_scangle_it 2.73 c_mcangle_it 1.99 c_scbond_it 1.74 c_angle_deg 1.5 c_mcbond_it 1.16 c_improper_angle_d 1.06 c_bond_d 0.008 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_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7270 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 404
Software Software Software Name Purpose CNS refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling CNS phasing