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Crystal structure of native Canavalia gladiata lectin (CGL): a tetrameric ConA-like lectin
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, HANGING DROP 8.5 293 ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.56 65.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.903 α = 90 b = 115.351 β = 90 c = 241.078 γ = 90
Symmetry Space Group C 2 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 MARRESEARCH 2004-05-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.43 LNLS D03B-MX1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 42.64 98.2 0.088 0.088 3.9 238197 57503 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.41 98.9 0.344 0.344 60.7 4 8944
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 2.3 10 2 238197 57503 3062 97.87 0.18632 0.18384 0.1874 0.23276 0.2326 RANDOM 20.654
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] -0.04 0.11 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 21.417 r_dihedral_angle_3_deg 17.969 r_dihedral_angle_1_deg 8.824 r_scangle_it 4.64 r_scbond_it 2.99 r_mcangle_it 2.182 r_angle_refined_deg 2.017 r_mcbond_it 1.25 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.819 r_dihedral_angle_4_deg 21.417 r_dihedral_angle_3_deg 17.969 r_dihedral_angle_1_deg 8.824 r_scangle_it 4.64 r_scbond_it 2.99 r_mcangle_it 2.182 r_angle_refined_deg 2.017 r_mcbond_it 1.25 r_nbtor_refined 0.32 r_symmetry_vdw_refined 0.276 r_nbd_refined 0.24 r_symmetry_hbond_refined 0.185 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.134 r_metal_ion_refined 0.082 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7220 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing