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Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of ubiquitin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other OTDUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 298 150 mM potassium thiocyanate, 32.5% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.81 56.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.745 α = 90 b = 144.074 β = 90 c = 143.474 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315 2019-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.98 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 70 97.5 0.102 0.119 0.06 9.5 3.6 121784
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 2.24 99 0.696 0.835 0.452 0.395 3.2
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 OTDUB 2.2 56.7 115715 5982 96.92 0.1778 0.1762 0.1983 0.2093 0.2225 RANDOM 58.856
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] -9.4 -2.83 12.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.351 r_dihedral_angle_4_deg 22.719 r_dihedral_angle_3_deg 20.826 r_dihedral_angle_1_deg 7.655 r_angle_refined_deg 1.861 r_angle_other_deg 1.375 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.351 r_dihedral_angle_4_deg 22.719 r_dihedral_angle_3_deg 20.826 r_dihedral_angle_1_deg 7.655 r_angle_refined_deg 1.861 r_angle_other_deg 1.375 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15348 Nucleic Acid Atoms Solvent Atoms 476 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing