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Three dimensional structure of the giant reed (Arundodonax) lectin (ADL)
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 Crystals were grown using the vapour diffusion hanging drop method by mixing equal volumes (1 uL) of the protein solution at concentration of 30 mg/ml and a solution 7.5 % in PEG 8000, 10% ethylene glycol and 0.1 M sodium cacodylate, pH 6.0 as the precipitant.
Crystal Properties Matthews coefficient Solvent content 3.27 62.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.04 α = 90 b = 127.04 β = 90 c = 46.49 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 1.7 30 99.6 0.073 11.3 5 47270
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 1.7 1.79 99.5 0.435 3.3 4.8
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 1.7 30 44903 2347 99.56 0.1624 0.1601 0.2059 0.2144 RANDOM 33.079
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] -0.91 -0.46 -0.91 2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.778 r_sphericity_free 21.961 r_sphericity_bonded 21.312 r_dihedral_angle_3_deg 13.742 r_rigid_bond_restr 9.472 r_dihedral_angle_4_deg 8.537 r_dihedral_angle_1_deg 6.703 r_angle_refined_deg 0.639 r_angle_other_deg 0.531 r_chiral_restr 0.045
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.778 r_sphericity_free 21.961 r_sphericity_bonded 21.312 r_dihedral_angle_3_deg 13.742 r_rigid_bond_restr 9.472 r_dihedral_angle_4_deg 8.537 r_dihedral_angle_1_deg 6.703 r_angle_refined_deg 0.639 r_angle_other_deg 0.531 r_chiral_restr 0.045 r_gen_planes_refined 0.017 r_bond_refined_d 0.005 r_gen_planes_other 0.003 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2250 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling MOLREP phasing