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Crystal structure of TONSL UBL domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q96HA7-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 100 mM Tris-bicine pH 8.5, 0.5% PEG monomethyl ether 5000, 0.8 M Potassium sodium tartrate tetrahydrate, 10 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.85 56.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.147 α = 90 b = 112.147 β = 90 c = 69.278 γ = 90
Symmetry Space Group I 4 2 2
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 Bruker PHOTON III 2022-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS DIAMOND MICROFOCUS 1.54
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 1.956 32.9 99.87 0.1174 0.1215 0.03132 0.999 18.07 15 15431 33.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2.08 99.92 1.769 0.484 0.627 1.61 14.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.96 32.9 15431 813 99.89 0.19461 0.19384 0.2045 0.20884 0.2193 RANDOM 41.734
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] -0.65 -0.65 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.449 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 6.275 r_long_range_B_other 6.163 r_scangle_other 3.362 r_mcangle_other 2.675 r_mcangle_it 2.674 r_scbond_it 2.003 r_scbond_other 1.999 r_mcbond_it 1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.449 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 6.275 r_long_range_B_other 6.163 r_scangle_other 3.362 r_mcangle_other 2.675 r_mcangle_it 2.674 r_scbond_it 2.003 r_scbond_other 1.999 r_mcbond_it 1.56 r_mcbond_other 1.559 r_angle_refined_deg 1.183 r_angle_other_deg 0.416 r_chiral_restr 0.059 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1282 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PROTEUM PLUS data collection XDS data reduction XSCALE data scaling PHASER phasing