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Structure of SapL1 lectin in complex with alpha methyl fucoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D4U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 292 1.5 M ammonium sulfate (NH4)2SO4
100 mM BICINE pH 8.5
12% Glycerol
10% Glycerol were added for cryoprotection
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.064 α = 90 b = 45.664 β = 105.054 c = 83.485 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER2 X 9M 2019-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.97857 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.4 39.99 98.2 0.085 0.118 0.082 0.991 5.3 2.7 21570
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 98.4 0.428 0.598 0.417 0.7 1.6 2.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4D4U 2.4 39.99 21561 1089 97.884 0.178 0.175 0.1826 0.2398 0.2392 33.358
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] -0.193 1.865 -0.899 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.615 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 14.251 r_dihedral_angle_1_deg 8.409 r_lrange_it 6.935 r_lrange_other 6.934 r_scangle_other 5.678 r_scangle_it 5.674 r_mcangle_other 5.301 r_mcangle_it 5.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.615 r_dihedral_angle_4_deg 15.444 r_dihedral_angle_3_deg 14.251 r_dihedral_angle_1_deg 8.409 r_lrange_it 6.935 r_lrange_other 6.934 r_scangle_other 5.678 r_scangle_it 5.674 r_mcangle_other 5.301 r_mcangle_it 5.298 r_scbond_it 4.183 r_scbond_other 4.175 r_mcbond_it 3.873 r_mcbond_other 3.866 r_angle_refined_deg 1.938 r_angle_other_deg 1.421 r_symmetry_nbd_other 0.209 r_nbd_refined 0.195 r_nbtor_refined 0.184 r_xyhbond_nbd_refined 0.16 r_symmetry_xyhbond_nbd_refined 0.159 r_nbd_other 0.154 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.087 r_symmetry_nbd_refined 0.055 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4442 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 155
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing