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Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with N-Acetyl glucosamine
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 3.23 61.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.55 α = 90 b = 127.55 β = 90 c = 45.6 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 2015-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 ESRF ID29
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 1.75 26.13 99.8 0.091 10.3 5.2 42913
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 1.75 1.84 99.7 0.393 3.4 4.9
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2X52 1.75 25.43 40867 2031 99.65 0.1503 0.1483 0.1709 0.19 0.189 RANDOM 30.51
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 0.22 0.44 -1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.538 r_sphericity_free 30.128 r_sphericity_bonded 15.126 r_dihedral_angle_3_deg 13.202 r_rigid_bond_restr 11.973 r_dihedral_angle_4_deg 8.069 r_dihedral_angle_1_deg 7.358 r_angle_refined_deg 0.581 r_angle_other_deg 0.496 r_chiral_restr 0.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.538 r_sphericity_free 30.128 r_sphericity_bonded 15.126 r_dihedral_angle_3_deg 13.202 r_rigid_bond_restr 11.973 r_dihedral_angle_4_deg 8.069 r_dihedral_angle_1_deg 7.358 r_angle_refined_deg 0.581 r_angle_other_deg 0.496 r_chiral_restr 0.044 r_gen_planes_refined 0.022 r_gen_planes_other 0.007 r_bond_refined_d 0.004 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 226 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing