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Crystal structure of recombinant dimeric Banana lectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BMY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 A protein solution [10 mg/mL, in 100 mM NaCl, 20mM Tris (pH 7.4)] was mixed 1:1 (v/v) with a reservoir solution containing 0.05 M NaBr, 0.1 M Bis Tris and 19% PEG 3350 (pH 7.5)
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.53 α = 90 b = 63.33 β = 90 c = 95.98 γ = 90
Symmetry Space Group P 2 21 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 PIXEL DECTRIS PILATUS 2M 2014-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92000 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 20 98.8 0.131 0.137 15.77 12.5 32288 -3 25.046
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 96.5 1.232 1.283 2.07
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 THROUGHOUT 2BMY 1.7 19.32 30642 1614 98.85 0.1691 0.1675 0.1815 0.198 0.2074 RANDOM 19.988
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] 0.62 -0.89 0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.879 r_dihedral_angle_3_deg 12.817 r_dihedral_angle_4_deg 10.166 r_dihedral_angle_1_deg 7.167 r_mcangle_it 2.808 r_angle_refined_deg 1.882 r_mcbond_it 1.878 r_mcbond_other 1.875 r_angle_other_deg 0.941 r_chiral_restr 0.124
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.879 r_dihedral_angle_3_deg 12.817 r_dihedral_angle_4_deg 10.166 r_dihedral_angle_1_deg 7.167 r_mcangle_it 2.808 r_angle_refined_deg 1.882 r_mcbond_it 1.878 r_mcbond_other 1.875 r_angle_other_deg 0.941 r_chiral_restr 0.124 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2056 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction