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Wisteria floribunda lectin in complex with GalNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XTM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291.15 0.2 M CaCl2,
0.1 M Bis-Tris pH 5.5,
45% (v/v) MPD
Crystal Properties Matthews coefficient Solvent content 2.54 51.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.191 α = 90 b = 157.269 β = 90 c = 55.73 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 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 2.32 30 99.8 0.083 0.089 0.035 7.6 7.2 45331
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 2.32 2.39 100 0.444 0.888 7.3 3705
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 4XTM 2.33 30 39349 2065 88.94 0.1864 0.1845 0.1896 0.2237 0.2243 RANDOM 38.267
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] -0.33 1.11 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.193 r_dihedral_angle_4_deg 21.026 r_dihedral_angle_3_deg 13.538 r_dihedral_angle_1_deg 7.184 r_mcangle_it 4.006 r_mcbond_it 2.58 r_mcbond_other 2.578 r_angle_refined_deg 1.558 r_angle_other_deg 0.968 r_chiral_restr 0.167
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.193 r_dihedral_angle_4_deg 21.026 r_dihedral_angle_3_deg 13.538 r_dihedral_angle_1_deg 7.184 r_mcangle_it 4.006 r_mcbond_it 2.58 r_mcbond_other 2.578 r_angle_refined_deg 1.558 r_angle_other_deg 0.968 r_chiral_restr 0.167 r_bond_refined_d 0.011 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 250 Heterogen Atoms 235
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction