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Crystal structure of the 5F-tryptophan RSL lectin in complex with Lewis x tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BT9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 Midas 1-30: 40% 5/4 PO/OH 100 mM Mes pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.35 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.883 α = 90 b = 129.883 β = 90 c = 129.883 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.93221 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.28 45.92 99.9 0.041 0.016 1 21.2 8.9 46835 11.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.28 1.3 99 0.456 0.192 0.944 3.9 8.1
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 2BT9 1.28 45.92 44461 2368 99.98 0.12366 0.12241 0.1226 0.14759 0.1483 RANDOM 14.353
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.622 r_sphericity_free 18.942 r_dihedral_angle_3_deg 11.209 r_dihedral_angle_1_deg 7.23 r_sphericity_bonded 6.705 r_dihedral_angle_4_deg 4.555 r_rigid_bond_restr 4.539 r_long_range_B_refined 2.475 r_long_range_B_other 2.325 r_scangle_other 2.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.622 r_sphericity_free 18.942 r_dihedral_angle_3_deg 11.209 r_dihedral_angle_1_deg 7.23 r_sphericity_bonded 6.705 r_dihedral_angle_4_deg 4.555 r_rigid_bond_restr 4.539 r_long_range_B_refined 2.475 r_long_range_B_other 2.325 r_scangle_other 2.058 r_angle_refined_deg 2.011 r_scbond_it 1.744 r_scbond_other 1.734 r_mcangle_other 1.716 r_mcangle_it 1.715 r_mcbond_other 1.42 r_mcbond_it 1.419 r_angle_other_deg 1.047 r_chiral_restr 0.105 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1374 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 163
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing