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B-trefoil lectin from Salpingoeca rosetta in complex with GalNAc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QE3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 292 0.1 M MOPSO, Bis-Tris pH 6.5, 100 mM AA Morpheus I, 25 % PEG SMEAR MEDIUM
Crystal Properties Matthews coefficient Solvent content 2.43 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.158 α = 90 b = 59.254 β = 90 c = 209.612 γ = 90
Symmetry Space Group P 21 21 21
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 2020-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980107 SOLEIL PROXIMA 1
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 1.7 45.19 100 0.078 0.089 0.041 0.999 14.6 8.5 79471
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 1.7 1.73 0.616 0.705 0.339 0.89 8.3
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 7QE3 1.7 44.28 79379 3914 99.963 0.171 0.1688 0.1684 0.2061 0.206 19.143
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] 1.285 -0.214 -1.071
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.247 r_dihedral_angle_4_deg 14.054 r_dihedral_angle_3_deg 11.98 r_dihedral_angle_1_deg 7.032 r_lrange_it 4.505 r_lrange_other 4.204 r_scangle_it 2.826 r_scangle_other 2.825 r_scbond_it 1.823 r_scbond_other 1.823
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.247 r_dihedral_angle_4_deg 14.054 r_dihedral_angle_3_deg 11.98 r_dihedral_angle_1_deg 7.032 r_lrange_it 4.505 r_lrange_other 4.204 r_scangle_it 2.826 r_scangle_other 2.825 r_scbond_it 1.823 r_scbond_other 1.823 r_mcangle_it 1.766 r_mcangle_other 1.766 r_angle_refined_deg 1.433 r_angle_other_deg 1.369 r_mcbond_it 1.183 r_mcbond_other 1.177 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.193 r_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.182 r_xyhbond_nbd_refined 0.166 r_nbtor_refined 0.159 r_ncsr_local_group_1 0.128 r_metal_ion_refined 0.122 r_symmetry_xyhbond_nbd_other 0.098 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5007 Nucleic Acid Atoms Solvent Atoms 977 Heterogen Atoms 123
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing