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Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with N,N'-Diacetylchitobiose; 30 seconds soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 7.5 % in PEG 8000, 10% ethylene glycol and 0.1 M sodium cacodylate, pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.25 62.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.08 α = 90 b = 127.08 β = 90 c = 46.14 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.91939 ESRF ID23-1
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 1.5 63.54 100 0.06 13 6.2 68370
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 1.5 1.58 99.9 0.429 3.1 5.8
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 2X52 1.5 30 64974 3347 99.93 0.1584 0.1566 0.1811 0.1928 0.1976 RANDOM 36.059
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] 0.54 0.27 0.54 -1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.514 r_sphericity_free 23.338 r_sphericity_bonded 20.139 r_dihedral_angle_4_deg 14.942 r_dihedral_angle_3_deg 13.655 r_rigid_bond_restr 12.434 r_dihedral_angle_1_deg 7.446 r_angle_other_deg 1.014 r_angle_refined_deg 0.725 r_chiral_restr 0.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.514 r_sphericity_free 23.338 r_sphericity_bonded 20.139 r_dihedral_angle_4_deg 14.942 r_dihedral_angle_3_deg 13.655 r_rigid_bond_restr 12.434 r_dihedral_angle_1_deg 7.446 r_angle_other_deg 1.014 r_angle_refined_deg 0.725 r_chiral_restr 0.047 r_gen_planes_refined 0.023 r_gen_planes_other 0.013 r_bond_refined_d 0.005 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing