☰ Navigation Tabs
The crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RFF PDB structure 1RFF
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 2.24 45.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.716 α = 90 b = 104.557 β = 90 c = 193.18 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 2003-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0781 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 2.22 50 92.7 0.081 21.25 5.84 47285 47285 -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) 2.22 2.278 80.3 0.39
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 structure 1RFF 2.22 50 47189 44791 2398 92.91 0.18931 0.18931 0.18709 0.1854 0.2308 0.2256 RANDOM 29.807
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] -0.72 1.98 -1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.185 r_scangle_it 3.917 r_scbond_it 2.59 r_mcangle_it 2.52 r_mcbond_it 1.489 r_angle_refined_deg 1.219 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.172 r_metal_ion_refined 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.185 r_scangle_it 3.917 r_scbond_it 2.59 r_mcangle_it 2.52 r_mcbond_it 1.489 r_angle_refined_deg 1.219 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.172 r_metal_ion_refined 0.129 r_symmetry_hbond_refined 0.1 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6820 Nucleic Acid Atoms 95 Solvent Atoms 184 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing