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Crystal Structure of Concanavalin A Complexed with Lysine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 2M Ammonium Sulphate, 0.1M Sodium Acetate (pH 5.0), PEG600 (5%), temperature 293.0 K
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.926 α = 90 b = 86.214 β = 90 c = 88.428 γ = 90
Symmetry Space Group I 2 2 2
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 Bruker PHOTON II 2024-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.22 21.87 99.9 0.114 0.162 0.975 18.1 1.9 12018 19.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.29 100 0.435 0.615 0.763 3.5 1.9
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 2.22 21.87 11448 570 99.83 0.19477 0.19203 0.2034 0.24839 0.2522 RANDOM 18.362
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] 1.35 -0.12 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.311 r_dihedral_angle_1_deg 8.089 r_dihedral_angle_2_deg 7.29 r_long_range_B_refined 4.647 r_long_range_B_other 4.625 r_scangle_other 2.904 r_mcangle_it 2.472 r_mcangle_other 2.471 r_scbond_it 1.783 r_scbond_other 1.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.311 r_dihedral_angle_1_deg 8.089 r_dihedral_angle_2_deg 7.29 r_long_range_B_refined 4.647 r_long_range_B_other 4.625 r_scangle_other 2.904 r_mcangle_it 2.472 r_mcangle_other 2.471 r_scbond_it 1.783 r_scbond_other 1.783 r_mcbond_it 1.472 r_mcbond_other 1.463 r_angle_refined_deg 1.314 r_angle_other_deg 0.463 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1809 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing