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Structure of the hexagonal form of the Boletus edulis lectin in complex with T-antigen disaccharide and N,N-diacetyl chitobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3QDW pdb entry 3QDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 0.2M ammonium acetate, 0.1M sodium acetate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.66 66.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.045 α = 90 b = 124.045 β = 90 c = 104.473 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 CCD ADSC QUANTUM 210r 2004-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM16 1.0 ESRF BM16
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 29.3 100 0.071 19.9 8.3 32555
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 2.11 100 0.285 7.9 7.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3QDW 2 29.27 30853 30853 1646 99.92 0.19292 0.1922 0.1935 0.2061 0.2062 RANDOM 22.502
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] 0.68 0.34 0.68 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.781 r_dihedral_angle_4_deg 12.321 r_dihedral_angle_3_deg 11.154 r_scangle_it 7.36 r_dihedral_angle_1_deg 5.275 r_scbond_it 5.14 r_mcangle_it 3.164 r_mcbond_it 2.241 r_angle_refined_deg 0.815 r_chiral_restr 0.055
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.781 r_dihedral_angle_4_deg 12.321 r_dihedral_angle_3_deg 11.154 r_scangle_it 7.36 r_dihedral_angle_1_deg 5.275 r_scbond_it 5.14 r_mcangle_it 3.164 r_mcbond_it 2.241 r_angle_refined_deg 0.815 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2240 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 82
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling