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Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with thymidine 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 = 73.646 α = 90 b = 73.646 β = 90 c = 106.375 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 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 99.4 0.056 17.7 4.9 27554
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) 1.8 1.86 99.4 0.35 3.9
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 26138 1386 99.49 0.17438 0.1725 0.1833 0.21016 0.2202 RANDOM 19.26
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] -0.36 -0.36 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.45 r_scangle_it 4.409 r_scbond_it 2.767 r_mcangle_it 2.007 r_angle_refined_deg 1.79 r_angle_other_deg 1.281 r_mcbond_it 1.144 r_symmetry_vdw_other 0.337 r_nbd_other 0.254 r_nbd_refined 0.222
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.45 r_scangle_it 4.409 r_scbond_it 2.767 r_mcangle_it 2.007 r_angle_refined_deg 1.79 r_angle_other_deg 1.281 r_mcbond_it 1.144 r_symmetry_vdw_other 0.337 r_nbd_other 0.254 r_nbd_refined 0.222 r_chiral_restr 0.118 r_symmetry_vdw_refined 0.115 r_xyhbond_nbd_refined 0.112 r_symmetry_hbond_refined 0.091 r_nbtor_other 0.089 r_gen_planes_other 0.02 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_metal_ion_refined 0.003 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 1602 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 23
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement