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Structure of the hexagonal form of the Boletus edulis lectin in complex with N-acetyl glucosamine and N-acetyl galactosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y2T pdb entry 1Y2T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 293 0.2M ammonium acetate, 0.1M sodium acetate, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.64 66.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.818 α = 90 b = 123.818 β = 90 c = 104.322 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 1.9 45 98.7 0.069 21.9 9.5 36987
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 1.9 2 99.6 0.266 9.3 9.4
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 1Y2T 1.9 40 35136 35136 1850 98.28 0.17891 0.17804 0.1787 0.1959 0.1933 RANDOM 21.972
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] 1.06 0.53 1.06 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.743 r_dihedral_angle_4_deg 13.355 r_dihedral_angle_3_deg 11.367 r_scangle_it 8.379 r_scbond_it 6.007 r_dihedral_angle_1_deg 5.402 r_mcangle_it 3.595 r_mcbond_it 2.595 r_angle_refined_deg 0.919 r_chiral_restr 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.743 r_dihedral_angle_4_deg 13.355 r_dihedral_angle_3_deg 11.367 r_scangle_it 8.379 r_scbond_it 6.007 r_dihedral_angle_1_deg 5.402 r_mcangle_it 3.595 r_mcbond_it 2.595 r_angle_refined_deg 0.919 r_chiral_restr 0.08 r_gen_planes_refined 0.007 r_bond_refined_d 0.005 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 129 Heterogen Atoms 60
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling