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Galectin-1 in complex with thiogalactoside derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Q27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 291 30% PEG 3350, 0.1 M Tris/HCl pH 8.0, 0.2 M Li2SO4, 1 % beta mercapthoethanol, seeded
Crystal Properties Matthews coefficient Solvent content 3.04 59.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.995 α = 90 b = 70.035 β = 90 c = 99.508 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 2020-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97625 MAX IV BioMAX
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 1.7 52.99 100 0.999 13.6 6.5 268479
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 1.7 1.73 0.666
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 1.7 46.82 39359 2113 99.94 0.17378 0.17241 0.184 0.20002 0.2082 RANDOM 33.952
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] -0.14 0.17 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.455 r_dihedral_angle_4_deg 18.833 r_dihedral_angle_3_deg 13.295 r_dihedral_angle_1_deg 7.757 r_long_range_B_refined 6.811 r_long_range_B_other 6.406 r_scangle_other 3.335 r_mcangle_it 2.347 r_mcangle_other 2.346 r_scbond_it 2.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.455 r_dihedral_angle_4_deg 18.833 r_dihedral_angle_3_deg 13.295 r_dihedral_angle_1_deg 7.757 r_long_range_B_refined 6.811 r_long_range_B_other 6.406 r_scangle_other 3.335 r_mcangle_it 2.347 r_mcangle_other 2.346 r_scbond_it 2.262 r_scbond_other 2.257 r_mcbond_it 1.461 r_mcbond_other 1.453 r_angle_refined_deg 1.423 r_angle_other_deg 1.33 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2118 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing