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Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyribouridine 5'-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 = 73.7 α = 90 b = 73.7 β = 90 c = 106.42 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 2003-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.98 20 100 0.08 23.6 15.1 21094 21057
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 1.98 2.1 98.8 0.36 7.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.98 20 21094 19972 1082 99.98 0.16564 0.16355 0.1766 0.20608 0.2148 RANDOM 26.509
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] -0.43 -0.43 0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.245 r_scangle_it 4.702 r_scbond_it 2.921 r_mcangle_it 2.107 r_angle_refined_deg 1.69 r_mcbond_it 1.116 r_angle_other_deg 0.933 r_symmetry_vdw_other 0.314 r_nbd_other 0.254 r_nbd_refined 0.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.245 r_scangle_it 4.702 r_scbond_it 2.921 r_mcangle_it 2.107 r_angle_refined_deg 1.69 r_mcbond_it 1.116 r_angle_other_deg 0.933 r_symmetry_vdw_other 0.314 r_nbd_other 0.254 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.145 r_chiral_restr 0.104 r_symmetry_vdw_refined 0.088 r_nbtor_other 0.086 r_bond_refined_d 0.019 r_gen_planes_other 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1597 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction XDS data scaling CNS phasing