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Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor pib-t
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 293 8% PEG 8000, 20MM DIHYDROGEN POTASSIUM PHOSPHATE, 10% GLYCEROL, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.81 α = 90 b = 73.81 β = 90 c = 105.51 γ = 90
Symmetry Space Group P 43 21 2
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 MARMOSAIC 225 mm CCD 2011-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.8 34.836 100 0.079 23.6 16.1 27645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 99.9 0.585 0.585 1.3 16
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 FOURIER SYNTHESIS THROUGHOUT 1.8 34.836 27581 1382 100 0.151 0.15 0.172 0.1776 RANDOM 26.04
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] 0.45 0.45 -0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.481 r_dihedral_angle_3_deg 13.123 r_dihedral_angle_4_deg 10.396 r_dihedral_angle_1_deg 5.929 r_angle_refined_deg 2.12 r_angle_other_deg 1.098 r_chiral_restr 0.132 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.481 r_dihedral_angle_3_deg 13.123 r_dihedral_angle_4_deg 10.396 r_dihedral_angle_1_deg 5.929 r_angle_refined_deg 2.12 r_angle_other_deg 1.098 r_chiral_restr 0.132 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1636 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling