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Structure of Tomato Bifunctional Nuclease TBN1, variant N211D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 0.1M Bis-Tris, 10% PEG 8000, 0.01M 5'-AMP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.05 59.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.944 α = 90 b = 115.944 β = 90 c = 74.713 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 CCD MARMOSAIC 225 mm CCD 2 MIRRORS AND A DOUBLE-CRYSTAL MONOCHROMATOR 2011-06-01 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 2.74 59.94 95.6 0.058 16.05 3.7 9436 9433 -3 56.5
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 2.74 2.9 81.5 0.536 1.54 2.5 1592
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 MOLECULAR REPLACEMENT Rfree throughout 4DJ4 2.74 41.71 9432 9432 475 95.68 0.19748 0.19748 0.1936 0.1837 0.2637 0.2161 random 66.592
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] 0.12 0.12 0.12 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.427 r_dihedral_angle_4_deg 16.188 r_dihedral_angle_3_deg 15.035 r_long_range_B_other 7.603 r_long_range_B_refined 7.602 r_dihedral_angle_1_deg 5.579 r_scangle_other 5.325 r_mcangle_it 5.309 r_mcangle_other 5.307 r_scbond_it 3.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.427 r_dihedral_angle_4_deg 16.188 r_dihedral_angle_3_deg 15.035 r_long_range_B_other 7.603 r_long_range_B_refined 7.602 r_dihedral_angle_1_deg 5.579 r_scangle_other 5.325 r_mcangle_it 5.309 r_mcangle_other 5.307 r_scbond_it 3.432 r_scbond_other 3.408 r_mcbond_it 3.396 r_mcbond_other 3.393 r_angle_refined_deg 1.413 r_angle_other_deg 0.807 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2145 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 97
Software Software Software Name Purpose MxCuBE data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling