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Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N 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 20% PEG3350, 0.1M HEPES, 0.2M magnesium sulfate, 5mM TCEP, 3% Hexanediol-1,6, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.453 α = 89.8 b = 82.036 β = 94.33 c = 98.677 γ = 112.78
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 2008-07-17 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 2.3 50 92.8 0.071 13.8 3.2 75956 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 2.3 2.38 97.3 0.241 3.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1Q32 2.3 50 75448 75448 3872 96.1 0.204 0.203 0.236 0.2458 RANDOM 53.87
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] 0.93 -0.97 1.22 -2.32 -1.26 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.846 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 16.404 r_dihedral_angle_1_deg 7.013 r_scangle_it 4.535 r_scbond_it 2.823 r_angle_refined_deg 1.907 r_mcangle_it 1.818 r_mcbond_it 0.961 r_chiral_restr 0.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.846 r_dihedral_angle_4_deg 17.958 r_dihedral_angle_3_deg 16.404 r_dihedral_angle_1_deg 7.013 r_scangle_it 4.535 r_scbond_it 2.823 r_angle_refined_deg 1.907 r_mcangle_it 1.818 r_mcbond_it 0.961 r_chiral_restr 0.134 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 13657 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling