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Structure of AcmJRL, a mannose binding jacalin related lectin from Ananas comosus, in complex with mannose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FLW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 4M sodium nitrate, 0.1 M Tris-HCl pH 8.5; protein solution 17mg/ml in H2O
Crystal Properties Matthews coefficient Solvent content 4.54 72.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.68 α = 90 b = 86.68 β = 90 c = 257.27 γ = 120
Symmetry Space Group P 61 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 PILATUS3 6M 2014-03-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9785 SOLEIL PROXIMA 1
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 2.749 48.842 99.9 0.196 13.2 12.4 28132
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 2.749 2.92 99.8 1.27 2 12.1
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 6FLW 2.749 48.842 1.35 28132 1415 99.86 0.1889 0.1872 0.1945 0.2211 0.2258 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 8.804 f_angle_d 0.981 f_chiral_restr 0.061 f_plane_restr 0.005 f_bond_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2174 Nucleic Acid Atoms Solvent Atoms 58 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing