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Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase 1 H432R Mutant (SCAN1 Mutant)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q32
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 291 24% PEG3350, 0.1M HEPES, 0.2M magnesium formate, 5mM TCEP, 2% Hexanediol-1,6, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.14 42.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.871 α = 89.52 b = 81.492 β = 84.9 c = 96.787 γ = 67.82
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD MARMOSAIC 225 mm CCD 2008-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 93.7 0.056 20.4 3.5 98077 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 74.5 0.287 3.7 3
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 (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 1Q32 2.1 24.79 93127 93126 4912 93.39 0.18939 0.18746 0.1835 0.22607 0.2235 RANDOM 48.743
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] 0.25 -0.83 0.78 -0.17 -1.1 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.049 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 14.685 r_dihedral_angle_1_deg 6.414 r_scangle_it 4.048 r_scbond_it 2.722 r_mcangle_it 1.772 r_angle_refined_deg 1.384 r_mcbond_it 0.996 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.049 r_dihedral_angle_4_deg 19.445 r_dihedral_angle_3_deg 14.685 r_dihedral_angle_1_deg 6.414 r_scangle_it 4.048 r_scbond_it 2.722 r_mcangle_it 1.772 r_angle_refined_deg 1.384 r_mcbond_it 0.996 r_chiral_restr 0.091 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13760 Nucleic Acid Atoms Solvent Atoms 472 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling