☰ Navigation Tabs
Concanavalin A bound to DNA glycoconjugates, Man-TTTT and Man-AAAA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CNA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 Sitting drop comprising 1 uL of Concanavalin A (32 uM), Man-TTTT (64 uM), and Man-AAAA (64 uM) + 1 uL crystallization condition (Helix screen, condition B5: 0.1 M lithium chloride, 0.01 M manganese(II) chloride tetrahydrate, 0.05 M MES (pH 6.5), 17% w/v PEG 4000). Reservoir contained 70 uL of crystallization condition
Crystal Properties Matthews coefficient Solvent content 2.69 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.979 α = 90 b = 70.18 β = 90 c = 124.42 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 CCD RAYONIX MX-300 2020-09-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.979 APS 21-ID-F
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 2.55 70.18 93.1 0.18 5.9147 3.25 17243
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 2.55 2.69 86 0.58 2.9
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 5CNA 2.55 70.18 17243 899 93.1 0.253 0.25 0.2529 0.314 0.3103 RANDOM 32.06
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] 0.33 1.28 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.009 r_dihedral_angle_3_deg 15.947 r_dihedral_angle_4_deg 12.445 r_dihedral_angle_1_deg 8.097 r_long_range_B_refined 7.579 r_long_range_B_other 7.559 r_scangle_other 4.489 r_mcangle_other 3.828 r_mcangle_it 3.826 r_scbond_it 2.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.009 r_dihedral_angle_3_deg 15.947 r_dihedral_angle_4_deg 12.445 r_dihedral_angle_1_deg 8.097 r_long_range_B_refined 7.579 r_long_range_B_other 7.559 r_scangle_other 4.489 r_mcangle_other 3.828 r_mcangle_it 3.826 r_scbond_it 2.833 r_scbond_other 2.833 r_mcbond_it 2.33 r_mcbond_other 2.323 r_angle_refined_deg 1.503 r_angle_other_deg 1.263 r_chiral_restr 0.153 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 3396 Nucleic Acid Atoms 164 Solvent Atoms 150 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing