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Concanavalin A bound to a DNA glycoconjugate, Man-AGCT
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 7 295 Sitting drop comprising 1 uL of Concanavalin A (40 uM) and Man-AGCT (160 uM) + 1 uL crystallization condition (Helix screen, condition D3: 0.2 M lithium sulfate, 0.05 M bis Tris (pH 7), 20% v/v MPD). Reservoir contained 70 uL of crystallization condition.
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.729 α = 90 b = 70.89 β = 90 c = 125.839 γ = 90
Symmetry Space Group P 21 2 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 9M 2020-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.0782 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 70.89 99.6 0.098 2.7065 8.75 61815
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 1.7 1.79 100 0.24 9.03
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 1.7 70.89 61815 3341 99.6 0.178 0.177 0.1866 0.207 0.2173 RANDOM 25.61
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] 1.16 0.11 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.581 r_dihedral_angle_4_deg 17.767 r_dihedral_angle_3_deg 12.387 r_dihedral_angle_1_deg 7.898 r_long_range_B_refined 7.499 r_long_range_B_other 7.407 r_scangle_other 6.099 r_scbond_it 3.936 r_scbond_other 3.935 r_mcangle_other 3.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.581 r_dihedral_angle_4_deg 17.767 r_dihedral_angle_3_deg 12.387 r_dihedral_angle_1_deg 7.898 r_long_range_B_refined 7.499 r_long_range_B_other 7.407 r_scangle_other 6.099 r_scbond_it 3.936 r_scbond_other 3.935 r_mcangle_other 3.14 r_mcangle_it 3.139 r_mcbond_it 2.208 r_mcbond_other 2.196 r_angle_refined_deg 1.689 r_angle_other_deg 1.516 r_chiral_restr 0.17 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 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 3551 Nucleic Acid Atoms 164 Solvent Atoms 441 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing