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X-ray structure of fully glycosylated bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AK0 PDB ID 1AK0 was used as a model for replacement into initial MAD maps.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 1.0 M Ammonium sulfate,
0.1 M BIS-TRIS pH 5.5,
1% w/v Polyethylene glycol 3,350, VAPOR DIFFUSION, HANGING DROP, temperature 291 K
Crystal Properties Matthews coefficient Solvent content 3.33 63.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.031 α = 90 b = 101.031 β = 90 c = 71.529 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2 mirrors and a double-crystal monochromator 2010-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 2.16 35 100 0.094 26.7 11.3 23089 23089 -3.7 36.2
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 2.16 2.24 100 0.597 4.5 11.1 2280
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 Combination of MAD and Molecular replacement Rfree throughout PDB ID 1AK0 was used as a model for replacement into initial MAD maps. 2.16 35 23002 23002 1182 99.63 0.18804 0.18804 0.18041 0.1899 0.22343 0.1984 random 31.642
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] 0.21 0.1 0.21 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.866 r_dihedral_angle_4_deg 16.612 r_dihedral_angle_3_deg 14.843 r_dihedral_angle_1_deg 5.549 r_angle_refined_deg 1.569 r_angle_other_deg 0.972 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.866 r_dihedral_angle_4_deg 16.612 r_dihedral_angle_3_deg 14.843 r_dihedral_angle_1_deg 5.549 r_angle_refined_deg 1.569 r_angle_other_deg 0.972 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2150 Nucleic Acid Atoms Solvent Atoms 140 Heterogen Atoms 151
Software Software Software Name Purpose MxCuBE data collection SHELX model building SHELXD phasing SHELXE model building MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing