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Entamoeba histolytica Gal/GalNAc lectin heavy chain residues 808-992 in the presence of galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9GEI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.05 M Sodium acetate, pH 4.0, 0.225 M Ammonium sulfate, 12 % w/v PEG 4000, 500 mM Gal + 20% glycerol
Crystal Properties Matthews coefficient Solvent content 3.63 66.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.239 α = 90 b = 146.315 β = 114 c = 85.328 γ = 90
Symmetry Space Group C 1 2 1
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 EIGER2 X 16M 2023-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim 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 1.818 77.95 93.6 0.044 0.996 10 6.9 52043
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.818 2 0.882 0.43
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 9GEI 1.818 36.07 52033 2527 62.3 0.2187 0.2173 0.2118 0.2459 0.2378 RANDOM 44.51
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] -2.7569 -2.4171 -2.6705 5.4274
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.36 t_omega_torsion 3.52 t_angle_deg 1.05 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.36 t_omega_torsion 3.52 t_angle_deg 1.05 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4398 Nucleic Acid Atoms Solvent Atoms 438 Heterogen Atoms 42
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction XDS data reduction STARANISO data scaling PHASER phasing