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Ubiquitin variant i53 in complex 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 6.4 293 0.1 M MES pH 6.4, 0.2 M Trimethylamine
N-oxide dehydrate, 2% w/v PEG2000
Crystal Properties Matthews coefficient Solvent content 1.89 34.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.37 α = 90 b = 46.86 β = 90 c = 90.32 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 EIGER X 9M TITANIUM SILICATE FLAT MIRROR WITH PT 2022-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.95372 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.21 25.33 96.93 0.05269 0.05672 0.02066 0.999 18.68 7.5 51451 12.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.21 1.23 93.5 0.952 7.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.21 25.3 51451 2573 96.93 0.1804 0.1857 0.1892 0.195 Random selection 16.47
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1538 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building SCALA data scaling PHASER phasing XDS data reduction