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Crystal structure of human Tyrosyl-DNA Phosphodiesterase complexed with vanadate, octopamine, and tetranucleotide AGTA
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 2.25 45.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.811 α = 90 b = 104.688 β = 90 c = 193.31 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 2.1 50 95.6 0.114 13.45 4.93 57880 -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 85.6 0.48 2.74
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 57538 54621 2917 95.76 0.197 0.197 0.19504 0.1973 0.23317 0.235 RANDOM 24.023
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 2.5 -1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.113 r_scangle_it 3.706 r_scbond_it 2.454 r_mcangle_it 2.422 r_mcbond_it 1.443 r_angle_refined_deg 1.343 r_angle_other_deg 0.495 r_nbd_other 0.365 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.247
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.113 r_scangle_it 3.706 r_scbond_it 2.454 r_mcangle_it 2.422 r_mcbond_it 1.443 r_angle_refined_deg 1.343 r_angle_other_deg 0.495 r_nbd_other 0.365 r_symmetry_hbond_refined 0.261 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.231 r_nbtor_other 0.181 r_xyhbond_nbd_refined 0.177 r_metal_ion_refined 0.097 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6846 Nucleic Acid Atoms 93 Solvent Atoms 222 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing