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Concanavalin A bound to a DNA glycoconjugate, Man-CGCG
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 (80 uM) and Man-CGCG (160 uM) + 1 uL crystallization condition (Helix screen, condition D9: 0.05 M bis-Tris (pH 7), 2 M ammonium sulfate, 5% v/v PEG 400). Reservoir contained 70 uL of crystallization condition
Crystal Properties Matthews coefficient Solvent content 2.78 55.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.419 α = 90 b = 69.92 β = 90 c = 125.869 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 2019-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1271 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3 69.92 98.18 0.197 0.209 2.5272 9.35 11395
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.16 99.97 0.66 0.693 10.05
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 3 69.92 11395 652 98.18 0.23605 0.23317 0.2443 0.28446 0.2819 RANDOM 57.774
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] -3.96 3.55 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_3_deg 14.973 r_scangle_other 9.973 r_dihedral_angle_1_deg 8.112 r_dihedral_angle_4_deg 7.942 r_mcangle_other 7.887 r_mcangle_it 7.885 r_scbond_it 6.63 r_scbond_other 6.628 r_mcbond_it 5.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.677 r_dihedral_angle_3_deg 14.973 r_scangle_other 9.973 r_dihedral_angle_1_deg 8.112 r_dihedral_angle_4_deg 7.942 r_mcangle_other 7.887 r_mcangle_it 7.885 r_scbond_it 6.63 r_scbond_other 6.628 r_mcbond_it 5.15 r_mcbond_other 5.134 r_angle_refined_deg 1.593 r_angle_other_deg 1.262 r_chiral_restr 0.169 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 3284 Nucleic Acid Atoms 164 Solvent Atoms 22 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing