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Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octapeptide KLNYYDPR, and tetranucleotide AGTT.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JY1 PDB entry 1jy1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 298 PEG 3000, NaCl, HEPES, spermine, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.23 44.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.076 α = 90 b = 104.904 β = 90 c = 193.832 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 CCD ADSC QUANTUM 4 2003-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.00 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.7 50 90.6 0.071 21.04 4.52 103225 103255 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 1.76 64.6 0.482 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1jy1 1.7 50 102833 97672 5161 90.78 0.19364 0.19364 0.19258 0.1919 0.21325 0.2137 RANDOM 24.569
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] -0.63 2 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.254 r_scangle_it 4.29 r_scbond_it 2.824 r_mcangle_it 2.754 r_mcbond_it 1.745 r_angle_refined_deg 1.335 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.156
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.254 r_scangle_it 4.29 r_scbond_it 2.824 r_mcangle_it 2.754 r_mcbond_it 1.745 r_angle_refined_deg 1.335 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.165 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.102 r_metal_ion_refined 0.1 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6933 Nucleic Acid Atoms 102 Solvent Atoms 343 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing