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High Resolution Structure of Concanavalin B from Jack Bean (Canavalia ensiformis), A Chitinase-like Protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 2% saturated ammonium sulfate buffered with Na phosphate at pH 6.5. Room temperature, crystallization in about 1 week. Protein dissolved in 5% NaCl and 0.1 M acetic acid.
Crystal Properties Matthews coefficient Solvent content 2.54 51.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.987 α = 90 b = 79.987 β = 90 c = 101.312 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 173 PIXEL DECTRIS PILATUS3 R CdTe 300K-W 2016-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 0.987 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.3 101.31 82 0.167 0.158 0.168 0.022 1 50.1 51.5 73116
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 18.1 0.85 0.78 0.918 0.331 0.71 3.6 5.5
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 1.3 69.27 69491 3565 81.87 0.09728 0.09574 0.1039 0.12778 0.1317 RANDOM 22.91
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] 0.03 0.02 0.03 -0.11
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.038 r_dihedral_angle_2_deg 36.089 r_sphericity_bonded 24.045 r_dihedral_angle_4_deg 23.049 r_dihedral_angle_3_deg 13.081 r_scangle_other 12.951 r_long_range_B_refined 11.774 r_long_range_B_other 11.031 r_scbond_other 10.715 r_scbond_it 10.713
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 51.038 r_dihedral_angle_2_deg 36.089 r_sphericity_bonded 24.045 r_dihedral_angle_4_deg 23.049 r_dihedral_angle_3_deg 13.081 r_scangle_other 12.951 r_long_range_B_refined 11.774 r_long_range_B_other 11.031 r_scbond_other 10.715 r_scbond_it 10.713 r_rigid_bond_restr 7.58 r_dihedral_angle_1_deg 6.039 r_mcangle_other 3.996 r_mcangle_it 3.973 r_mcbond_it 3.184 r_mcbond_other 3.088 r_angle_refined_deg 1.561 r_angle_other_deg 0.977 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.004 r_gen_planes_other 0.003 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2298 Nucleic Acid Atoms Solvent Atoms 344 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing