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Crystal structure of a recombinant Vatairea macrocarpa seed lectin complexed with Tn antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4U2A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 Cubic-like crystals
Crystal Properties Matthews coefficient Solvent content 3.04 59.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.093 α = 90 b = 86.024 β = 90 c = 128.877 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 DECTRIS PILATUS 6M 2013-12-13 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 1.968 71.55 97.7 0.112 0.122 0.049 10 6.2 22033
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 1.97 2.07 85.3 0.521 0.521 0.229 1.3 5.8 2762
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 4U2A 1.97 71.55 20674 1123 96.68 0.2007 0.1979 0.2074 0.2544 0.2008 RANDOM 29.233
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] -1.93 2.67 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_3_deg 15.041 r_sphericity_free 9.363 r_dihedral_angle_4_deg 6.997 r_dihedral_angle_1_deg 6.254 r_rigid_bond_restr 4.989 r_sphericity_bonded 4.748 r_mcbond_it 2.694 r_mcbond_other 2.668 r_mcangle_it 2.614
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.165 r_dihedral_angle_3_deg 15.041 r_sphericity_free 9.363 r_dihedral_angle_4_deg 6.997 r_dihedral_angle_1_deg 6.254 r_rigid_bond_restr 4.989 r_sphericity_bonded 4.748 r_mcbond_it 2.694 r_mcbond_other 2.668 r_mcangle_it 2.614 r_angle_other_deg 2.359 r_angle_refined_deg 1.463 r_chiral_restr 0.088 r_bond_refined_d 0.014 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1811 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction PHASER phasing Coot model building iMOSFLM data reduction