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Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor PMcP-U
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MH9 PDB entry 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 2.63 52.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.758 α = 90 b = 73.758 β = 90 c = 105.981 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 2001-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.933 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 30 209551
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1MH9 1.4 25.32 37528 35599 1929 64.83 0.13503 0.13337 0.1363 0.16454 RANDOM 17.719
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] 0.16 0.16 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.325 r_sphericity_free 5.48 r_scangle_it 4.797 r_sphericity_bonded 3.822 r_scbond_it 3.304 r_mcangle_it 2.586 r_rigid_bond_restr 1.947 r_angle_refined_deg 1.856 r_mcbond_it 1.73 r_angle_other_deg 1.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.325 r_sphericity_free 5.48 r_scangle_it 4.797 r_sphericity_bonded 3.822 r_scbond_it 3.304 r_mcangle_it 2.586 r_rigid_bond_restr 1.947 r_angle_refined_deg 1.856 r_mcbond_it 1.73 r_angle_other_deg 1.008 r_nbd_refined 0.501 r_symmetry_vdw_other 0.385 r_symmetry_vdw_refined 0.301 r_symmetry_hbond_refined 0.29 r_nbd_other 0.252 r_xyhbond_nbd_refined 0.249 r_chiral_restr 0.132 r_nbtor_other 0.086 r_bond_refined_d 0.02 r_gen_planes_other 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1602 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing