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Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RFF PDB entry 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 2.26 45.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.8 α = 90 b = 104.711 β = 90 c = 193.751 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 2002-12-01 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 2.1 50 94.2 0.108 10.5 3.19 56460 -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) 2.1 2.18 91.7 0.601 1.8
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 1RFF 2.1 50 56410 53558 2852 93.98 0.20144 0.20144 0.19944 0.2002 0.23903 0.2362 RANDOM 28.839
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] -0.81 1.45 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.299 r_scangle_it 3.846 r_scbond_it 2.583 r_mcangle_it 2.5 r_mcbond_it 1.53 r_angle_refined_deg 1.245 r_nbd_other 0.42 r_nbtor_other 0.333 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.213
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.299 r_scangle_it 3.846 r_scbond_it 2.583 r_mcangle_it 2.5 r_mcbond_it 1.53 r_angle_refined_deg 1.245 r_nbd_other 0.42 r_nbtor_other 0.333 r_symmetry_vdw_refined 0.27 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.196 r_angle_other_deg 0.184 r_chiral_restr 0.091 r_metal_ion_refined 0.046 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6818 Nucleic Acid Atoms 102 Solvent Atoms 198 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing