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Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JY1 PDB structure 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 2.26 45.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.791 α = 90 b = 104.894 β = 90 c = 194.124 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 0.9791 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 2 50 97.4 0.085 15.29 4.15 68032 -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) 2 2.07 91.2 0.368 3.38
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 MIR THROUGHOUT PDB structure 1JY1 2 50 67981 64557 3424 97.46 0.19595 0.19595 0.19428 0.1961 0.22761 0.2286 RANDOM 23.713
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] -1.4 2.7 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.157 r_scangle_it 3.745 r_scbond_it 2.481 r_mcangle_it 2.382 r_mcbond_it 1.457 r_angle_refined_deg 1.161 r_angle_other_deg 0.762 r_nbd_other 0.437 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.157 r_scangle_it 3.745 r_scbond_it 2.481 r_mcangle_it 2.382 r_mcbond_it 1.457 r_angle_refined_deg 1.161 r_angle_other_deg 0.762 r_nbd_other 0.437 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.209 r_nbtor_other 0.192 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.176 r_metal_ion_refined 0.109 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6827 Nucleic Acid Atoms 100 Solvent Atoms 222 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing