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Structure of human POT1 DNA binding domain bound to a 5'-phosphorylated junction of a telomeric DNA hairpin with a 3'-overhang
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XJV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 hDBD complex with 5prime-p-hp-ss1-12 was crystallized at 16C by the hanging drop method in a drop containing 0.8 microliter of 13 mg/ml protein-DNA complex (in 25 mM Tris (pH 8), 100 mM NaCl, and 2 mM DTT) and 0.8 microliter well solution (0.1 M NaOAc (pH 5.2) and 10% PEG 20,000). Crystals were harvested in 25 mM Tris (pH 8), 100 mM NaCl, 0.1 M NaOAc (pH 5.2), and 10% PEG 20,000 and cryoprotected in harvesting solution supplemented with 30% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.33 47.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.23 α = 90 b = 67.23 β = 90 c = 143.373 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER2 X 9M 2022-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.12723 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.16 71.69 100 0.086 0.999 19.6 19.3 20897
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.16 2.23 1.131 0.858
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.16 45.19 1.34 20846 1745 99.96 0.1818 0.18 0.1811 0.2214 0.2208 63.64
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 18.9007 f_angle_d 0.6461 f_chiral_restr 0.0443 f_plane_restr 0.0043 f_bond_d 0.0034
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2339 Nucleic Acid Atoms 420 Solvent Atoms 120 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing