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Crystal Structure of Concanavalin A Complexed with 5-Fluorouracil
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DQ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293.5 0. 1M Sodium Accetate buffer pH 5.0 , 5% PEG 6000, 2 M Ammonium Sulphate.
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.781 α = 90 b = 86.546 β = 90 c = 88.637 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 PIXEL Bruker PHOTON II 2023-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.5406
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.94 20.74 99.7 0.175 0.91 11.8 1.8 5189
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.94 3.14 100 0.296 0.722 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.96 20.74 4905 283 99.58 0.19918 0.19477 0.2083 0.27389 0.2702 RANDOM 5.397
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] 3.04 -1.99 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.14 r_dihedral_angle_2_deg 11.783 r_dihedral_angle_1_deg 9.339 r_long_range_B_refined 2.677 r_long_range_B_other 2.676 r_mcangle_it 1.457 r_mcangle_other 1.456 r_angle_refined_deg 1.422 r_scangle_other 1.089 r_mcbond_it 0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.14 r_dihedral_angle_2_deg 11.783 r_dihedral_angle_1_deg 9.339 r_long_range_B_refined 2.677 r_long_range_B_other 2.676 r_mcangle_it 1.457 r_mcangle_other 1.456 r_angle_refined_deg 1.422 r_scangle_other 1.089 r_mcbond_it 0.776 r_mcbond_other 0.776 r_scbond_it 0.581 r_scbond_other 0.554 r_angle_other_deg 0.484 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 1809 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data reduction Aimless data scaling MOLREP phasing