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Structure of Boletus edulis lectin in complex with 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 6.5 293 0.2M magnesium acetate, 0.1M sodium cacodylate, 10% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.72 54.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.174 α = 90 b = 84.058 β = 90 c = 120.165 γ = 90
Symmetry Space Group P 21 21 21
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 210 2007-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
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 39.7 99.9 0.075 17 5.4 47335
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 0.243 6.3 5.4
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 PDB ENTRY 3QDW 2 39.67 44892 2392 99.8 0.201 0.199 0.2 0.24 0.2408 RANDOM 21.56
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] 3.63 -1.61 -2.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.303 r_dihedral_angle_3_deg 10.976 r_dihedral_angle_4_deg 9.624 r_scangle_it 5.924 r_dihedral_angle_1_deg 4.949 r_scbond_it 4.18 r_mcangle_it 2.308 r_mcbond_it 1.515 r_angle_refined_deg 0.731 r_chiral_restr 0.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.303 r_dihedral_angle_3_deg 10.976 r_dihedral_angle_4_deg 9.624 r_scangle_it 5.924 r_dihedral_angle_1_deg 4.949 r_scbond_it 4.18 r_mcangle_it 2.308 r_mcbond_it 1.515 r_angle_refined_deg 0.731 r_chiral_restr 0.049 r_bond_refined_d 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4480 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 116
Software Software Software Name Purpose REFMAC refinement ADSC data collection AMoRE phasing MOSFLM data reduction SCALA data scaling