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Wisteria floribunda lectin in complex with GalNAc(beta1-4)GlcNAc (LacdiNAc) at pH 4.2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KXC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 291.15 0.2 M Lithium Sulfate
0.1 M phosphate-citrate pH 4.2
20% (w/v) PEG 1000
Crystal Properties Matthews coefficient Solvent content 2.67 53.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.584 α = 90 b = 97.943 β = 90 c = 149.158 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 2.09 50.01 100 0.145 0.156 0.057 5.9 7.5 67430
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.15 100 0.774 0.833 0.305 0.86 7.5 5548
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 5KXC 2.09 50.01 63779 3413 99.63 0.1822 0.1806 0.189 0.2117 0.2188 RANDOM 28.467
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] 0.38 0.04 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 20.33 r_dihedral_angle_3_deg 12.627 r_dihedral_angle_1_deg 7.168 r_mcangle_it 2.441 r_mcbond_it 1.567 r_mcbond_other 1.566 r_angle_refined_deg 1.558 r_angle_other_deg 0.991 r_chiral_restr 0.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_4_deg 20.33 r_dihedral_angle_3_deg 12.627 r_dihedral_angle_1_deg 7.168 r_mcangle_it 2.441 r_mcbond_it 1.567 r_mcbond_other 1.566 r_angle_refined_deg 1.558 r_angle_other_deg 0.991 r_chiral_restr 0.179 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 568 Heterogen Atoms 383
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction