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Galectin-3 in complex with Methyl 2,6-anhydro-3-deoxy-3-S-(b-D-galactopyranosyl)-3-thio-D-glycero-L-altro-heptonate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 289 0.1 M Tris-HCl, pH 8.5, 0.2 M MgCl2, and 35% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.07 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.94 α = 90 b = 57.87 β = 90 c = 62.65 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 IMAGE PLATE MAR scanner 345 mm plate 2020-10-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.75 35.94 99.9 0.995 12.7 4.5 13748
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 0.962
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 (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 1.75 31.19 13111 600 99.88 0.15639 0.15377 0.1556 0.21357 0.2157 RANDOM 16.21
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] -0.89 -0.07 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.742 r_dihedral_angle_4_deg 13.464 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_1_deg 7.23 r_long_range_B_refined 5.865 r_angle_refined_deg 1.959 r_scbond_it 1.259 r_mcangle_it 1.124 r_mcbond_it 0.709 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.742 r_dihedral_angle_4_deg 13.464 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_1_deg 7.23 r_long_range_B_refined 5.865 r_angle_refined_deg 1.959 r_scbond_it 1.259 r_mcangle_it 1.124 r_mcbond_it 0.709 r_chiral_restr 0.126 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1108 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling REFMAC phasing