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Crystal structure of the 4-FLUORO RSL lectin in complex with Lewis x tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O7V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 Morpheus 1-9: 60mM divalent, 100 mM buffer pH 7.5, 20% peg550MME and 10M peg20K
Crystal Properties Matthews coefficient Solvent content 2.39 48.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.465 α = 90 b = 130.465 β = 90 c = 130.465 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 PILATUS3 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 1.35 19.9 99.5 0.052 0.023 0.995 22.6 6.8 40182
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 1.35 1.37 98 0.164 0.074 0.984 8.7 6.6
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 5o7V 1.35 19.9 38130 2052 99.53 0.12799 0.12654 0.1266 0.15573 0.1551 RANDOM 6.173
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 37.633 r_dihedral_angle_1_deg 29.9 r_sphericity_free 20.877 r_dihedral_angle_3_deg 11.261 r_sphericity_bonded 4.49 r_dihedral_angle_4_deg 3.469 r_long_range_B_refined 2.195 r_rigid_bond_restr 1.961 r_angle_refined_deg 1.803 r_long_range_B_other 1.672
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.633 r_dihedral_angle_1_deg 29.9 r_sphericity_free 20.877 r_dihedral_angle_3_deg 11.261 r_sphericity_bonded 4.49 r_dihedral_angle_4_deg 3.469 r_long_range_B_refined 2.195 r_rigid_bond_restr 1.961 r_angle_refined_deg 1.803 r_long_range_B_other 1.672 r_scangle_other 1.01 r_angle_other_deg 0.95 r_scbond_it 0.876 r_scbond_other 0.875 r_mcangle_it 0.772 r_mcangle_other 0.772 r_mcbond_it 0.606 r_mcbond_other 0.606 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 1378 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing