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Crystal structure of the tetragonal form of the common edible mushroom (Agaricus bisporus) lectin in complex with T-antigen and N-acetylglucosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other STRUCTURE OF UNLIGANDED LECTIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 PEG 8000, lithium sulfate, isopropanol, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.7 66.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.675 α = 90 b = 85.675 β = 90 c = 257.073 γ = 90
Symmetry Space Group P 43 21 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 MARRESEARCH Silicon toroidal mirror coated with Rhodium 2004-07-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.923 ESRF ID23-1
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 2.35 30 99.7 0.079 5.5 7.9 40259 40259
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 2.36 2.44 98.6 0.167 3.5
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 (All) 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 STRUCTURE OF UNLIGANDED LECTIN 2.36 30 38380 38380 2028 99.78 0.22881 0.22881 0.22756 0.2313 0.25241 0.2552 RANDOM 26.169
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] 0.44 0.44 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.167 r_scangle_it 1.853 r_angle_refined_deg 1.215 r_scbond_it 1.144 r_mcangle_it 0.732 r_mcbond_it 0.373 r_nbd_refined 0.177 r_symmetry_hbond_refined 0.142 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.167 r_scangle_it 1.853 r_angle_refined_deg 1.215 r_scbond_it 1.144 r_mcangle_it 0.732 r_mcbond_it 0.373 r_nbd_refined 0.177 r_symmetry_hbond_refined 0.142 r_symmetry_vdw_refined 0.127 r_chiral_restr 0.116 r_xyhbond_nbd_refined 0.098 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 4540 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing