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Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine and trinucleotide GTT
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 2.27 45.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.692 α = 90 b = 104.75 β = 90 c = 194.033 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 2.3 50 99.1 0.118 13.72 4.9 46407 46407 -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) 2.3 2.36 50.5 0.505 2.53
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 2.3 50 45642 43330 2312 99.12 0.19052 0.19052 0.18819 0.1869 0.2347 0.2307 RANDOM 27.645
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] -1.19 2.59 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.279 r_scangle_it 4.053 r_scbond_it 2.712 r_mcangle_it 2.616 r_mcbond_it 1.523 r_angle_refined_deg 1.241 r_nbd_other 0.428 r_nbtor_other 0.237 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.279 r_scangle_it 4.053 r_scbond_it 2.712 r_mcangle_it 2.616 r_mcbond_it 1.523 r_angle_refined_deg 1.241 r_nbd_other 0.428 r_nbtor_other 0.237 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.186 r_angle_other_deg 0.12 r_metal_ion_refined 0.12 r_symmetry_hbond_refined 0.102 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6820 Nucleic Acid Atoms 80 Solvent Atoms 227 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing