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Crystal structure of TOPBP1 BRCT4,5 in complex with a 53BP1 phosphopeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UEN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 287.15 10% w/v PEG 4000, 20% v/v glycerol
0.02 M of each carboxylic acid
0.1 M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 4.45 72.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.81 α = 90 b = 134.81 β = 90 c = 303.02 γ = 120
Symmetry Space Group P 65 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 DECTRIS PILATUS3 6M 2013-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3.53 67.405 100 21.03 70.6 20816
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.53 3.656 100
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 3UEN 3.53 67.405 1.34 20813 1047 99.97 0.2216 0.221 0.2261 0.2338 0.2375
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 3.966 f_angle_d 2.444 f_chiral_restr 0.124 f_bond_d 0.023 f_plane_restr 0.02
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6078 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing