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Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor NPB-T
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L6A PDB ENTRY 4L6A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 20 mM potassium phosphate monobasic, 8% PEG8000, 10% glycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.1 60.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.65 α = 90 b = 73.65 β = 90 c = 105.91 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 RAYONIX MX-225 2012-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.97826 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.375 52.078 90.9 0.041 26.11 56940 -3 23.35
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.375 1.45 61.9 0.674 1.91
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4L6A 1.375 46.73 56839 2886 92.95 0.1538 0.1526 0.1525 0.176 0.1761 RANDOM 22.2308
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] -0.11 -0.11 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.933 r_dihedral_angle_4_deg 12.02 r_dihedral_angle_3_deg 11.733 r_dihedral_angle_1_deg 6.006 r_mcangle_it 2.602 r_angle_refined_deg 2.044 r_mcbond_it 1.627 r_mcbond_other 1.626 r_angle_other_deg 0.955 r_chiral_restr 0.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.933 r_dihedral_angle_4_deg 12.02 r_dihedral_angle_3_deg 11.733 r_dihedral_angle_1_deg 6.006 r_mcangle_it 2.602 r_angle_refined_deg 2.044 r_mcbond_it 1.627 r_mcbond_other 1.626 r_angle_other_deg 0.955 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1633 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 123
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XDS data scaling