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Ubiquitin variant i53:Mutant T12Y.T14E.L67R with 53BP1 Tudor domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5J26
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 290 0.1 M MES pH 6.0,
0.2 M Trimethylamine N-oxide dehydrate,
13% w/v PEG MME 2000
Crystal Properties Matthews coefficient Solvent content 1.93 36.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.511 α = 90 b = 46.855 β = 90 c = 91.122 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 PIXEL DECTRIS PILATUS3 6M 2023-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97939 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.751 29.85 98.89 0.06022 0.0653 0.02474 0.999 12.41 6.6 17557 33.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.751 1.813 94.24 0.9374 0.386 3.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.751 29.85 17497 843 98.915 0.225 0.2224 0.2285 0.2725 0.2748 43.643
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] 0.232 -0.488 0.255
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.266 r_dihedral_angle_6_deg 14.709 r_lrange_other 7.844 r_lrange_it 7.841 r_dihedral_angle_1_deg 7.225 r_scangle_it 6.024 r_scangle_other 6.021 r_dihedral_angle_2_deg 5.676 r_mcangle_other 4.256 r_mcangle_it 4.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.266 r_dihedral_angle_6_deg 14.709 r_lrange_other 7.844 r_lrange_it 7.841 r_dihedral_angle_1_deg 7.225 r_scangle_it 6.024 r_scangle_other 6.021 r_dihedral_angle_2_deg 5.676 r_mcangle_other 4.256 r_mcangle_it 4.25 r_scbond_other 3.837 r_scbond_it 3.836 r_mcbond_it 2.93 r_mcbond_other 2.929 r_angle_refined_deg 1.348 r_angle_other_deg 0.452 r_nbd_other 0.23 r_symmetry_nbd_refined 0.219 r_nbd_refined 0.217 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.162 r_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.064 r_bond_refined_d 0.007 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 1535 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building SCALA data scaling PHASER phasing XDS data reduction