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Concanavalin A crystallized in the presence of Gal-ATAT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Sitting drop comprising 1 uL of Concanavalin A (32 uM) and Gal-ATAT (128 uM) + 1 uL crystallization condition (Helix screen, condition H9: 0.1 M potassium chloride, 0.002 M spermine tetrahydrochloride, 0.05 M bis-Tris (pH 7.5), 7% w/v PEG 8000). Reservoir contained 70 uL of crystallization condition.
Crystal Properties Matthews coefficient Solvent content 2.31 46.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.63 α = 90 b = 86.03 β = 90 c = 89.23 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 CCD RAYONIX MX-300 2020-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.9786 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) 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 61.93 93.4 0.114 0.123 3.0684 7.66 14558
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 84.7 0.45 7.05
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 1JBC 2 61.93 14558 749 93.4 0.182 0.179 0.1911 0.237 0.2377 RANDOM 19.4
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] 1.54 -0.34 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.727 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 11.848 r_dihedral_angle_1_deg 8.703 r_long_range_B_refined 5.521 r_long_range_B_other 5.251 r_scangle_other 2.967 r_mcangle_it 2.423 r_mcangle_other 2.422 r_scbond_it 1.938
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.727 r_dihedral_angle_4_deg 17.918 r_dihedral_angle_3_deg 11.848 r_dihedral_angle_1_deg 8.703 r_long_range_B_refined 5.521 r_long_range_B_other 5.251 r_scangle_other 2.967 r_mcangle_it 2.423 r_mcangle_other 2.422 r_scbond_it 1.938 r_scbond_other 1.934 r_mcbond_it 1.618 r_mcbond_other 1.614 r_angle_refined_deg 1.566 r_angle_other_deg 1.335 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 1769 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing