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Galectin-3 with a bound inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2.4 M Sodium malonate
pH 7.0
(Index/C3)
Crystal Properties Matthews coefficient Solvent content 1.95 36.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.41 α = 90 b = 57.8 β = 90 c = 62.13 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 PILATUS 2M-F 2021-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.15 42.319 99.8 0.111 0.999 9.83 6.3 44848
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.22 99.5 2.79 0.207 6.09
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.25 42.304 35000 1740 99.877 0.166 0.1639 0.1748 0.2043 0.2129 15.096
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] -2.239 1.273 0.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.839 r_lrange_it 13.201 r_lrange_other 12.302 r_dihedral_angle_3_deg 11.053 r_scangle_it 8.471 r_scangle_other 8.424 r_dihedral_angle_1_deg 7.427 r_dihedral_angle_2_deg 6.508 r_mcangle_it 6.142 r_mcangle_other 6.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.839 r_lrange_it 13.201 r_lrange_other 12.302 r_dihedral_angle_3_deg 11.053 r_scangle_it 8.471 r_scangle_other 8.424 r_dihedral_angle_1_deg 7.427 r_dihedral_angle_2_deg 6.508 r_mcangle_it 6.142 r_mcangle_other 6.142 r_scbond_it 5.86 r_scbond_other 5.81 r_mcbond_it 4.393 r_mcbond_other 4.286 r_rigid_bond_restr 3.649 r_angle_refined_deg 1.705 r_angle_other_deg 0.615 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.208 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.173 r_nbd_other 0.15 r_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.143 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.088 r_chiral_restr_other 0.013 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1102 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing