☰ Navigation Tabs
Concanavalin A bound to a DNA glycoconjugate, Man-AAATTT
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 6.5 295 Sitting drop comprising 1 uL of Concanavalin A (32 uM) and Man-AAATTT (64 uM) + 1 uL crystallization condition (Helix screen, condition A3: 0.1 M sodium chloride, 0.05 M lithium chloride, 0.01 M magnesium chloride hexahydrate, 0.05 M MES (pH 6.5), 25% v/v PEG 400). Reservoir contained 70 uL of crystallization condition
Crystal Properties Matthews coefficient Solvent content 2.91 57.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.09 α = 90 b = 77.78 β = 90 c = 126.06 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 2020-10-21 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) 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 57.9 90.1 0.107 4.6593 3.16 37677
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 83.4 0.7 3.16
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 57.9 37677 2002 90.1 0.198 0.196 0.2028 0.229 0.2317 RANDOM 27.55
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] 0.3 1.32 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.463 r_dihedral_angle_3_deg 12.475 r_dihedral_angle_4_deg 9.837 r_dihedral_angle_1_deg 8.124 r_long_range_B_refined 7.525 r_long_range_B_other 7.472 r_scangle_other 5.544 r_scbond_it 3.737 r_scbond_other 3.736 r_mcangle_other 3.627
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.463 r_dihedral_angle_3_deg 12.475 r_dihedral_angle_4_deg 9.837 r_dihedral_angle_1_deg 8.124 r_long_range_B_refined 7.525 r_long_range_B_other 7.472 r_scangle_other 5.544 r_scbond_it 3.737 r_scbond_other 3.736 r_mcangle_other 3.627 r_mcangle_it 3.626 r_mcbond_it 2.439 r_mcbond_other 2.436 r_angle_refined_deg 1.623 r_angle_other_deg 1.395 r_chiral_restr 0.176 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 3465 Nucleic Acid Atoms 246 Solvent Atoms 288 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing