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Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PAU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4YIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 291 100mM CHES, pH 9.5, 20% PEG8000
Crystal Properties Matthews coefficient Solvent content 3.11 60.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.858 α = 90 b = 73.858 β = 90 c = 106.121 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 PIXEL DECTRIS PILATUS 6M 2015-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) CC (Half) 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 1.37 46.86 99.9 0.061 1 23.56 10.1 62295 22.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.45 99.7 1.248 0.683 1.93 10.2
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 4YIK 1.37 46.86 60197 2100 99.91 0.1258 0.1249 0.1245 0.1505 0.1495 RANDOM 20.552
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] -0.39 -0.39 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.252 r_sphericity_free 20.301 r_dihedral_angle_4_deg 14.986 r_rigid_bond_restr 11.219 r_dihedral_angle_3_deg 11.093 r_sphericity_bonded 7.614 r_dihedral_angle_1_deg 5.873 r_angle_other_deg 2.263 r_angle_refined_deg 2.117 r_chiral_restr 0.198
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.252 r_sphericity_free 20.301 r_dihedral_angle_4_deg 14.986 r_rigid_bond_restr 11.219 r_dihedral_angle_3_deg 11.093 r_sphericity_bonded 7.614 r_dihedral_angle_1_deg 5.873 r_angle_other_deg 2.263 r_angle_refined_deg 2.117 r_chiral_restr 0.198 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1608 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 62
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction