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Crystal structure of the complex of Tdp1 with duplex DNA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JY1 pdbid 1JY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 0.1M Ammonium sulphate, 0.1M HEPES, 25% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.39 48.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.01 α = 90 b = 195.31 β = 90 c = 50.83 γ = 90
Symmetry Space Group P 21 21 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 S 6M 2015-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.04 52.05 99.2 15.3 9.6 69045
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdbid 1JY1 2.04 52.05 65640 3336 99.22 0.2338 0.2319 0.2359 0.2709 0.2774 RANDOM 56.481
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] 1.37 0.12 -1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.797 r_dihedral_angle_3_deg 18.438 r_dihedral_angle_4_deg 18.004 r_dihedral_angle_1_deg 8.376 r_angle_refined_deg 1.261 r_angle_other_deg 0.722 r_chiral_restr 0.081 r_gen_planes_refined 0.014 r_bond_refined_d 0.01 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.797 r_dihedral_angle_3_deg 18.438 r_dihedral_angle_4_deg 18.004 r_dihedral_angle_1_deg 8.376 r_angle_refined_deg 1.261 r_angle_other_deg 0.722 r_chiral_restr 0.081 r_gen_planes_refined 0.014 r_bond_refined_d 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6894 Nucleic Acid Atoms 169 Solvent Atoms 57 Heterogen Atoms
Software Software Software Name Purpose xia2 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction PHASER phasing xia2 data reduction