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Isolectin B4 from Vicia villosa in complex with the Tn antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other structure of unliganded lectin (from reference 1)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 291 acetate, MPD , pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.84 56.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.51 α = 90 b = 85.51 β = 90 c = 153.65 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 AREA DETECTOR MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LURE BEAMLINE DW32 0.93 LURE DW32
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.7 20 99.8 0.107 4.7 30037
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.8 99.8 0.46
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT structure of unliganded lectin (from reference 1) 2.7 20 28662 28662 1505 99.9 0.19034 0.18787 0.23766 RANDOM 33.566
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] 0.34 0.34 -0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.311 r_dihedral_angle_1_deg 4.485 r_scangle_it 2.786 r_angle_refined_deg 1.696 r_scbond_it 1.689 r_mcangle_it 1.227 r_mcbond_it 0.644 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.311 r_dihedral_angle_1_deg 4.485 r_scangle_it 2.786 r_angle_refined_deg 1.696 r_scbond_it 1.689 r_mcangle_it 1.227 r_mcbond_it 0.644 r_nbd_refined 0.253 r_symmetry_vdw_refined 0.191 r_xyhbond_nbd_refined 0.136 r_chiral_restr 0.103 r_metal_ion_refined 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6992 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 244
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement