☰ Navigation Tabs
Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)
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 = 73.77 α = 90 b = 73.77 β = 90 c = 106.057 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 2.05 20 99.7 0.073 21.5 6.1 18971
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) 2.05 2.12 100 0.376 4.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.05 20 17970 976 99.84 0.17601 0.17417 0.21032 0.2103 RANDOM 25.206
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] -0.6 -0.6 1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.519 r_scangle_it 4.721 r_scbond_it 2.986 r_mcangle_it 2.018 r_angle_refined_deg 1.672 r_mcbond_it 1.11 r_angle_other_deg 0.936 r_symmetry_vdw_other 0.375 r_xyhbond_nbd_refined 0.317 r_symmetry_vdw_refined 0.283
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.519 r_scangle_it 4.721 r_scbond_it 2.986 r_mcangle_it 2.018 r_angle_refined_deg 1.672 r_mcbond_it 1.11 r_angle_other_deg 0.936 r_symmetry_vdw_other 0.375 r_xyhbond_nbd_refined 0.317 r_symmetry_vdw_refined 0.283 r_nbd_other 0.256 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.111 r_nbtor_other 0.088 r_bond_refined_d 0.02 r_gen_planes_other 0.016 r_gen_planes_refined 0.012 r_metal_ion_refined 0.008 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 165 Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement