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X-ray structure of SPOP MATH domain (D140G) in complex with a 53BP1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 SPOP MATH was at 24 mg/ml and 1:5 protein:53BP1 peptide molar ratio.
Crystals were grown by the hanging drop method, mixing 2 ul of the protein sample in 20 mM Tris-HCl, pH 7.6, 150 mM NaCl, 5 mM DTT and 2 ul of the reservoir solution for the drop. The reservoir solution was 0.5 ml. Reservoir solution: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 0.2 M (NH4)2SO4, 1 M Li2SO4
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.657 α = 90 b = 90.724 β = 90 c = 92.819 γ = 90
Symmetry Space Group C 2 2 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 210r 2019-02-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.9794 APS 19-BM
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 1.44 24.32 98.21 0.032 0.034 0.012 1 43.35 8.1 33113 14.36
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 1.44 1.49 97.15 0.15 0.17 0.06 0.985 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3HQM 1.44 24.32 1.34 33113 2000 98.22 0.1685 0.1673 0.168 0.1862 0.1872 23.33
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.1988 f_angle_d 0.8732 f_chiral_restr 0.0816 f_bond_d 0.0058 f_plane_restr 0.0049
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1152 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 5
Software Software Software Name Purpose HKL-3000 data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing Coot model building PHENIX refinement