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Crystal structure of type-I ribosome-inactivating protein trichobakin (TBK)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JJR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 8mM sodium citrate pH 5.0, 10% KCl.
Crystal Properties Matthews coefficient Solvent content 2.11 41.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.72 α = 90 b = 73.73 β = 96.85 c = 88.07 γ = 90
Symmetry Space Group P 1 21 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 MAR CCD 165 mm 2019-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.79475 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 39.41 99.8 0.2 0.219 0.087 0.992 6.4 6 61634
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 98.9 0.7 0.764 0.302 0.846 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2JJR 2 39.41 58630 2986 99.79 0.1748 0.1722 0.1818 0.2265 0.2314 RANDOM 13.117
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] 8.18 -3.45 0.18 -8.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.785 r_dihedral_angle_4_deg 19.648 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 6.693 r_angle_refined_deg 1.862 r_angle_other_deg 1.47 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.785 r_dihedral_angle_4_deg 19.648 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_1_deg 6.693 r_angle_refined_deg 1.862 r_angle_other_deg 1.47 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7577 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction