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Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H432N_Glu 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 17% PEG3350, 0.1M HEPES, 0.2M magnesium sulfate, 5mM TCEP, 5% Hexanediol-1,6, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.22 44.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.35 α = 86.79 b = 82.19 β = 85.57 c = 99.29 γ = 66.32
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 300 mm CCD 2007-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
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 50 95.9 0.067 24.7 1.9 119602 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 2.07 81.3 0.357 3.6 1.7
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 50 115913 115913 6070 97.2 0.176 0.174 0.1748 0.213 0.2125 RANDOM 44.59
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] -1.63 0.86 -0.05 -0.05 0.36 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.769 r_dihedral_angle_4_deg 22.22 r_dihedral_angle_3_deg 15.001 r_dihedral_angle_1_deg 6.83 r_scangle_it 6.304 r_scbond_it 3.87 r_mcangle_it 3.465 r_rigid_bond_restr 2.405 r_mcbond_it 1.988 r_angle_refined_deg 1.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.769 r_dihedral_angle_4_deg 22.22 r_dihedral_angle_3_deg 15.001 r_dihedral_angle_1_deg 6.83 r_scangle_it 6.304 r_scbond_it 3.87 r_mcangle_it 3.465 r_rigid_bond_restr 2.405 r_mcbond_it 1.988 r_angle_refined_deg 1.958 r_chiral_restr 0.144 r_bond_refined_d 0.024 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13884 Nucleic Acid Atoms Solvent Atoms 744 Heterogen Atoms 35
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction DPS data reduction