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Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 8.5.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291.15 0.1 M Tris-HCl pH 8.5
25% (v/v) PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.93 58.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.745 α = 90 b = 103.383 β = 90 c = 148.922 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 CCD MARMOSAIC 300 mm CCD Vertical Focusing Mirror 2015-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 30 100 0.095 0.102 0.043 7.9 7.3 114273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 100 0.655 0.722 7.4 9412
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 5KXB 1.8 30 108425 5635 99.78 0.1981 0.197 0.2057 0.2192 0.2259 RANDOM 30.988
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] 1.68 0.97 -2.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_4_deg 24.529 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 7.11 r_mcangle_it 2.834 r_mcbond_it 1.988 r_mcbond_other 1.987 r_angle_refined_deg 1.631 r_angle_other_deg 1.024 r_chiral_restr 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.353 r_dihedral_angle_4_deg 24.529 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 7.11 r_mcangle_it 2.834 r_mcbond_it 1.988 r_mcbond_other 1.987 r_angle_refined_deg 1.631 r_angle_other_deg 1.024 r_chiral_restr 0.172 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7404 Nucleic Acid Atoms Solvent Atoms 654 Heterogen Atoms 261
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data reduction