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B-trefoil lectin from Salpingoeca rosetta in complex with Gb3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QE4
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 amino acids Morpheus I, 35 % PEG SMEAR MEDIUM
Crystal Properties Matthews coefficient Solvent content 2.403 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.341 α = 90 b = 58.997 β = 90 c = 210.306 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 2021-10-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.978565 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 1.84 45.18 99.8 0.093 0.106 0.05 0.999 11.8 8.2 62904
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 1.84 1.88 1.034 1.185 0.572 0.792 7.8
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 7QE4 1.84 45.18 62818 2982 99.755 0.187 0.1844 0.1813 0.2396 0.2365 27.838
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] 2.658 -1.087 -1.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_4_deg 16.464 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 7.599 r_lrange_it 6.748 r_lrange_other 6.673 r_scangle_it 5.544 r_scangle_other 5.544 r_scbond_it 4.148 r_scbond_other 4.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.779 r_dihedral_angle_4_deg 16.464 r_dihedral_angle_3_deg 13.207 r_dihedral_angle_1_deg 7.599 r_lrange_it 6.748 r_lrange_other 6.673 r_scangle_it 5.544 r_scangle_other 5.544 r_scbond_it 4.148 r_scbond_other 4.148 r_mcangle_it 4.089 r_mcangle_other 4.089 r_mcbond_it 3.214 r_mcbond_other 3.214 r_angle_refined_deg 2.103 r_angle_other_deg 1.487 r_nbd_other 0.231 r_symmetry_xyhbond_nbd_other 0.223 r_symmetry_nbd_refined 0.212 r_nbd_refined 0.199 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.171 r_ncsr_local_group_1 0.129 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4956 Nucleic Acid Atoms Solvent Atoms 604 Heterogen Atoms 140
Software Software Software Name Purpose REFMAC refinement REFMAC refinement Aimless data scaling PHASER phasing BUCCANEER model building XDS data reduction