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Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-monophosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 PEG8000, potassium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.453 α = 90 b = 73.453 β = 90 c = 106.085 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 2004-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 40 98.4 0.061 27.3 8.2 27294
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 98.8 0.37 4.7
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.8 40 25876 1369 98.43 0.17398 0.17248 0.1858 0.2018 0.2149 RANDOM 20.844
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] -0.35 -0.35 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.312 r_scangle_it 4.365 r_scbond_it 2.787 r_mcangle_it 1.839 r_angle_refined_deg 1.614 r_mcbond_it 1.026 r_angle_other_deg 0.904 r_symmetry_vdw_other 0.351 r_symmetry_vdw_refined 0.257 r_nbd_other 0.249
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.312 r_scangle_it 4.365 r_scbond_it 2.787 r_mcangle_it 1.839 r_angle_refined_deg 1.614 r_mcbond_it 1.026 r_angle_other_deg 0.904 r_symmetry_vdw_other 0.351 r_symmetry_vdw_refined 0.257 r_nbd_other 0.249 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.113 r_xyhbond_nbd_refined 0.094 r_nbtor_other 0.086 r_metal_ion_refined 0.074 r_bond_refined_d 0.017 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other 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 1597 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing