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Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor DPB-T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MH9 pdb code 1MH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.3 298 PEG 8000, potassium phosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.64 53.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.651 α = 90 b = 73.651 β = 90 c = 106.83 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 ADSC QUANTUM 4 2002-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
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 pdb code 1MH9 1.6 19.77 38484 38484 3859 97.7 0.186 0.186 0.1856 0.206 0.2053 RANDOM 26
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] -1.62 -1.62 3.25
RMS Deviations Key Refinement Restraint Deviation c_scbond_it 26.96 c_dihedral_angle_d 23.9 c_scangle_it 14.32 c_mcangle_it 3.77 c_mcbond_it 3.04 c_angle_deg 2.2 c_improper_angle_d 1.48 c_bond_d 0.026
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1598 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 34
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing