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Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 5'-monophosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.572 α = 90 b = 73.572 β = 90 c = 105.748 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 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 1.7 40 98.5 0.047 24.5 5 32144
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 1.7 1.76 98.3 0.334 3.7
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 1.7 40 30463 1624 98.49 0.19403 0.19291 0.1907 0.21527 0.2131 RANDOM 24.348
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] -0.28 -0.28 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.469 r_dihedral_angle_4_deg 16.438 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_1_deg 5.866 r_scangle_it 3.935 r_scbond_it 2.554 r_mcangle_it 1.739 r_angle_refined_deg 1.631 r_mcbond_it 1.051 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.469 r_dihedral_angle_4_deg 16.438 r_dihedral_angle_3_deg 13.953 r_dihedral_angle_1_deg 5.866 r_scangle_it 3.935 r_scbond_it 2.554 r_mcangle_it 1.739 r_angle_refined_deg 1.631 r_mcbond_it 1.051 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.137 r_chiral_restr 0.105 r_xyhbond_nbd_refined 0.105 r_bond_refined_d 0.015 r_metal_ion_refined 0.009 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_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 163 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement