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Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with sialic acid
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 3.2 61.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.21 α = 90 b = 127.21 β = 90 c = 45.37 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 1.6 63.6 99.9 0.062 12 5.9 55614
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 1.6 1.69 100 0.434 3 5.9
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 1.6 30 52733 2789 99.78 0.1922 0.1914 0.2069 0.212 RANDOM 36.375
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] -0.16 -0.08 -0.16 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.313 r_dihedral_angle_3_deg 13.719 r_dihedral_angle_4_deg 8.062 r_dihedral_angle_1_deg 6.095 r_angle_refined_deg 0.598 r_angle_other_deg 0.497 r_chiral_restr 0.04 r_gen_planes_refined 0.024 r_gen_planes_other 0.01 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.313 r_dihedral_angle_3_deg 13.719 r_dihedral_angle_4_deg 8.062 r_dihedral_angle_1_deg 6.095 r_angle_refined_deg 0.598 r_angle_other_deg 0.497 r_chiral_restr 0.04 r_gen_planes_refined 0.024 r_gen_planes_other 0.01 r_bond_refined_d 0.006 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing