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Crystal structure of native lectin from Platypodium elegans seeds (PELa) complexed with Man1-3Man-OMe.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZVX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.9 293 100 mM Bicine pH 8.9
10% PEG 20000
3% 1,4-dioxane
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.24 α = 90 b = 87.51 β = 90 c = 120.12 γ = 90
Symmetry Space Group C 2 2 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 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) 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 1.6 26.62 99.8 0.123 0.123 0.136 0.056 0.992 7.2 5.4 37353 37353 9.75
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 1.6 1.69 99.8 0.435 0.623 3.7
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ZVX 1.6 26.62 1.33 37305 1821 99.77 0.1851 0.1839 0.2078 0.1946 15.2183
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 15.702 f_angle_d 0.856 f_chiral_restr 0.059 f_bond_d 0.031 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1892 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 40
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing