☰ Navigation Tabs
Concanavalin A crystallized in the presence of Man-8
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 (32 uM) and mannose-squaramide (128 uM) + 1 uL crystallization condition (Helix screen, condition B6: 0.1 M sodium chloride, 0.005 M strontium chloride hexahydrate, 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 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.42 α = 90 b = 86.13 β = 90 c = 89.5 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) 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 1.8 62.06 99.8 0.148 2.5465 9.11 21234
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 1.8 1.9 100 0.63 8.95
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 1.8 62.06 21234 1114 99.8 0.186 0.184 0.1941 0.23 0.2331 RANDOM 17.64
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] 1.69 -0.34 -1.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.37 r_dihedral_angle_4_deg 20.881 r_dihedral_angle_3_deg 11.852 r_dihedral_angle_1_deg 8.359 r_long_range_B_refined 5.943 r_long_range_B_other 5.577 r_scangle_other 3.02 r_mcangle_it 2.261 r_mcangle_other 2.26 r_scbond_it 1.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.37 r_dihedral_angle_4_deg 20.881 r_dihedral_angle_3_deg 11.852 r_dihedral_angle_1_deg 8.359 r_long_range_B_refined 5.943 r_long_range_B_other 5.577 r_scangle_other 3.02 r_mcangle_it 2.261 r_mcangle_other 2.26 r_scbond_it 1.971 r_scbond_other 1.965 r_angle_refined_deg 1.56 r_mcbond_it 1.463 r_mcbond_other 1.458 r_angle_other_deg 1.369 r_chiral_restr 0.066 r_bond_refined_d 0.01 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 1761 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing