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Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with N,N'-Diacetylchitobiose; 60 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 3.22 61.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.96 α = 90 b = 126.96 β = 90 c = 45.87 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 1.8 63.48 99.9 0.108 10.5 6.1 39380
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 1.8 1.9 99.8 0.564 3.9 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2X52 1.8 30 37303 1998 99.61 0.1754 0.1741 0.2012 0.2164 RANDOM 33.355
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] -1.28 -0.64 -1.28 4.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.444 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_4_deg 7.751 r_dihedral_angle_1_deg 5.642 r_angle_refined_deg 0.518 r_angle_other_deg 0.498 r_gen_planes_refined 0.025 r_chiral_restr 0.024 r_gen_planes_other 0.014 r_bond_refined_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.444 r_dihedral_angle_3_deg 12.749 r_dihedral_angle_4_deg 7.751 r_dihedral_angle_1_deg 5.642 r_angle_refined_deg 0.518 r_angle_other_deg 0.498 r_gen_planes_refined 0.025 r_chiral_restr 0.024 r_gen_planes_other 0.014 r_bond_refined_d 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing