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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 VAPOR DIFFUSION, SITTING DROP 288 0.1 M sodium acetate pH 6.2, 29 % PEG 4000, 0.2 M ammonium sulphate, seeded
Crystal Properties Matthews coefficient Solvent content 2.79 55.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.139 α = 90 b = 62.352 β = 90 c = 98.016 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 6M 2018-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.54 46.72 99.9 0.054 0.999 10 4.24 48869
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.57 0.76 0.51
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.54 46.715 48869 2453 99.814 0.177 0.1752 0.2189 0.2089 31.666
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] 2.112 0.725 -2.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.638 r_dihedral_angle_3_deg 14.19 r_lrange_it 11.438 r_lrange_other 10.887 r_dihedral_angle_2_deg 7.932 r_dihedral_angle_1_deg 7.554 r_scangle_it 7.112 r_scangle_other 7.096 r_rigid_bond_restr 6.189 r_mcangle_it 5.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.638 r_dihedral_angle_3_deg 14.19 r_lrange_it 11.438 r_lrange_other 10.887 r_dihedral_angle_2_deg 7.932 r_dihedral_angle_1_deg 7.554 r_scangle_it 7.112 r_scangle_other 7.096 r_rigid_bond_restr 6.189 r_mcangle_it 5.687 r_mcangle_other 5.686 r_scbond_it 5.175 r_scbond_other 5.102 r_mcbond_it 3.993 r_mcbond_other 3.991 r_angle_refined_deg 2.093 r_angle_other_deg 0.655 r_symmetry_nbd_refined 0.296 r_nbd_other 0.248 r_symmetry_xyhbond_nbd_refined 0.235 r_nbd_refined 0.216 r_symmetry_nbd_other 0.208 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.18 r_ncsr_local_group_1 0.117 r_symmetry_nbtor_other 0.092 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2040 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing