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Crystal Structure Analysis of the Yeast Tyrosyl-DNA Phosphodiesterase H182A 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 VAPOR DIFFUSION, SITTING DROP 7.8 277 20% PEG3350, 0.1M HEPES, 0.2M Calcium Chloride, 5mM TCEP, 5% Hexanendiol-1,6, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 44.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.148 α = 86.92 b = 81.786 β = 85.53 c = 98.585 γ = 67.1
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 2008-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 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 2.4 50 50 0.064 10.1 2.2 69246 69246 2 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 2.4 2.49 95.3 0.435 2.2 2.1
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 2.5 50 57928 57928 3095 95.84 0.20631 0.20501 0.2052 0.23054 0.231 RANDOM 74.116
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] 5.44 0.71 1.11 -4.58 -0.99 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.347 r_dihedral_angle_4_deg 18.279 r_dihedral_angle_3_deg 17.411 r_dihedral_angle_1_deg 6.812 r_scangle_it 5.485 r_mcangle_it 3.266 r_scbond_it 3.242 r_angle_refined_deg 1.811 r_mcbond_it 1.712 r_chiral_restr 0.125
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.347 r_dihedral_angle_4_deg 18.279 r_dihedral_angle_3_deg 17.411 r_dihedral_angle_1_deg 6.812 r_scangle_it 5.485 r_mcangle_it 3.266 r_scbond_it 3.242 r_angle_refined_deg 1.811 r_mcbond_it 1.712 r_chiral_restr 0.125 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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 13667 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling