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Crystal structure of a lectin from Canavalia brasiliensis seed (ConBr) complexed with indole-3-acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 1.8 M ammonium sulfate, 0.2 M sodium chloride, 0.1 M HEPES, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.39 48.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.806 α = 90 b = 72.427 β = 90 c = 99.272 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 2017-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 49.69 98.3 0.046 0.048 0.013 1 30.4 11.9 12527
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 88.8 0.212 0.225 0.073 0.994 8.9 8.9
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 FREE R-VALUE 3JU9 2.2 49.69 11864 660 98.21 0.2005 0.1985 0.204 0.2356 0.2468 RANDOM 45.966
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] -0.49 3.32 -2.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.426 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_4_deg 12.655 r_dihedral_angle_1_deg 8.569 r_angle_refined_deg 1.274 r_angle_other_deg 1.169 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.426 r_dihedral_angle_3_deg 13.668 r_dihedral_angle_4_deg 12.655 r_dihedral_angle_1_deg 8.569 r_angle_refined_deg 1.274 r_angle_other_deg 1.169 r_chiral_restr 0.044 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1775 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOLREP phasing SCALA data scaling XDS data reduction MxCuBE data collection