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Crystal Structure of Native Lectin from Canavalia bonariensis Seeds (CaBo) complexed with alpha-methyl-D-mannoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OVU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.8 293 100 mM Sodium Acetate, pH 4.8
10% PEG 3000
400 mM Zync Acetate
Crystal Properties Matthews coefficient Solvent content 2.45 49.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.169 α = 90 b = 70.03 β = 90 c = 111.649 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 DECTRIS PILATUS 2M 2016-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.42 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 36.093 99.6 0.108 0.108 0.992 9.5 5.9 11449 22.93
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 2.3 2.42 99.1 0.25 0.949 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2OVU 2.3 36.093 1.35 11360 602 98.61 0.231 0.228 0.2422 0.2829 0.2883 24.5989
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.876 f_angle_d 1.068 f_chiral_restr 0.067 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 15
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing