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Crystal structure of a seed lectin from Vatairea macrocarpa complexed with Tn-antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FNZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 Citric acid buffers, ammonium sulphate.
Crystal Properties Matthews coefficient Solvent content 2.87 57.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.076 α = 90 b = 85.808 β = 90 c = 129.057 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 PSI PILATUS 6M 2013-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.915 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.398 71.455 99.5 0.059 0.064 0.025 18.6 6.5 61513 61513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.47 96.9 0.268 0.268 0.115 2.8 6.3 8641
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 1FNZ 1.4 71.46 61844 3117 99.47 0.179 0.178 0.1862 0.1968 0.2006 RANDOM 13.798
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] 0.58 0.73 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.829 r_dihedral_angle_3_deg 12.201 r_sphericity_free 11.106 r_dihedral_angle_4_deg 8.643 r_rigid_bond_restr 8.135 r_dihedral_angle_1_deg 5.919 r_sphericity_bonded 3.917 r_angle_other_deg 2.827 r_angle_refined_deg 1.547 r_mcbond_it 1.435
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.829 r_dihedral_angle_3_deg 12.201 r_sphericity_free 11.106 r_dihedral_angle_4_deg 8.643 r_rigid_bond_restr 8.135 r_dihedral_angle_1_deg 5.919 r_sphericity_bonded 3.917 r_angle_other_deg 2.827 r_angle_refined_deg 1.547 r_mcbond_it 1.435 r_mcangle_it 1.433 r_mcbond_other 1.382 r_chiral_restr 0.098 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1777 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing