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Se-M variant of B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA (Arg, Thr, Lys, His), 45 % precipitant mix 6 Morpheus II-2
Crystal Properties Matthews coefficient Solvent content 3 59.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.99 α = 90 b = 58.579 β = 90.682 c = 166.424 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 EIGER X 16M 2020-10-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9788 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.2 39.775 99.5 0.095 0.12 0.072 0.996 11.2 4.9 44177
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 2.2 2.27 98.3 0.503 0.634 0.383 0.852 3 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MAD FREE R-VALUE 2.2 39.775 44117 2095 99.403 0.185 0.1824 0.2312 0.2242 31.486
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] 0.042 1.775 -1.792 1.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.464 r_dihedral_angle_4_deg 16.772 r_dihedral_angle_3_deg 16.667 r_lrange_it 8.53 r_lrange_other 8.525 r_dihedral_angle_1_deg 7.891 r_scangle_it 6.803 r_scangle_other 6.802 r_mcangle_it 5.201 r_mcangle_other 5.201
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.464 r_dihedral_angle_4_deg 16.772 r_dihedral_angle_3_deg 16.667 r_lrange_it 8.53 r_lrange_other 8.525 r_dihedral_angle_1_deg 7.891 r_scangle_it 6.803 r_scangle_other 6.802 r_mcangle_it 5.201 r_mcangle_other 5.201 r_scbond_it 4.538 r_scbond_other 4.537 r_mcbond_it 3.596 r_mcbond_other 3.595 r_angle_refined_deg 1.92 r_angle_other_deg 1.372 r_symmetry_nbd_refined 0.223 r_nbd_other 0.215 r_nbd_refined 0.196 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.155 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.062 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4983 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction SHELX model building SHELX phasing CRANK2 phasing BUCCANEER model building