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Structure of Colocasia Esculenta Agglutinin with mannose bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 298 50 molar excess of D-Mannose was added to the purified 8.10 mg/ml lectin stock solution; 2 vols of this was mixed with 1 vol of crystallizing agent containing 0.1 M sodium citrate tribasic pH 5.6 and 1.0 M ammonium phosphate monobasic; equilibrated with above crystallizing agent in reservoir; large crystals in 3 weeks
Crystal Properties Matthews coefficient Solvent content 4.23 70.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.896 α = 90 b = 75.896 β = 90 c = 124.065 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 111 IMAGE PLATE RIGAKU RAXIS IV++ 2014-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5419
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.7 29.04 85.6 0.313 4 9.13 39501
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 24.7 0.664 1.3 3.62
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3R0E 1.85 19.803 1.37 35187 698 97.95 0.3166 0.3156 0.3244 0.3693 0.3731 Random selection
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 14.922 f_angle_d 1.536 f_chiral_restr 0.085 f_bond_d 0.011 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1716 Nucleic Acid Atoms Solvent Atoms 33 Heterogen Atoms 65
Software Software Software Name Purpose PHENIX refinement d*TREK data reduction d*TREK data scaling MOLREP phasing