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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 2NN8
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 1.93 36.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.49 α = 90 b = 57.74 β = 90 c = 61.53 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 4M 2020-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.9998 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 30.765 98.9 0.073 0.998 7.26 3.15 83428
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 1.01 0.457 0.7 2.55
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 1.2 30.702 39160 1958 99.941 0.164 0.1623 0.1792 0.1863 0.2009 17.305
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] -2.003 -1.388 3.391
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.901 r_dihedral_angle_3_deg 12.231 r_lrange_it 10.619 r_lrange_other 9.6 r_dihedral_angle_1_deg 7.619 r_scangle_it 5.875 r_scangle_other 5.86 r_dihedral_angle_2_deg 4.883 r_mcangle_it 4.727 r_mcangle_other 4.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.901 r_dihedral_angle_3_deg 12.231 r_lrange_it 10.619 r_lrange_other 9.6 r_dihedral_angle_1_deg 7.619 r_scangle_it 5.875 r_scangle_other 5.86 r_dihedral_angle_2_deg 4.883 r_mcangle_it 4.727 r_mcangle_other 4.727 r_scbond_it 3.993 r_scbond_other 3.985 r_mcbond_it 3.249 r_mcbond_other 3.226 r_rigid_bond_restr 2.883 r_angle_refined_deg 1.262 r_chiral_restr_other 1.083 r_angle_other_deg 0.593 r_symmetry_nbd_other 0.196 r_nbd_refined 0.193 r_symmetry_nbd_refined 0.174 r_nbtor_refined 0.168 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.121 r_symmetry_xyhbond_nbd_refined 0.105 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.07 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1104 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing