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Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4L57 PDB ENTRY 4L57
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 293 40 mM potassium phosphate monobasic, 6% PEG8000, 20% gycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.818 α = 111.18 b = 46.451 β = 88.16 c = 61.738 γ = 104.7
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 MARMOSAIC 225 mm CCD 2012-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 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 1.82 57.443 95.8 0.046 12.27 2.11 33500 -3 34.274
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 1.82 1.93 94.1 0.462 2.09
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4L57 1.82 57.44 33458 1672 96.11 0.1868 0.1847 0.1918 0.2278 0.2313 RANDOM 36.8837
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] -0.82 -0.58 -0.2 0.69 0.87 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.563 r_dihedral_angle_4_deg 19.675 r_dihedral_angle_3_deg 13.029 r_dihedral_angle_1_deg 6.248 r_mcangle_it 2.693 r_angle_refined_deg 2.083 r_mcbond_it 1.987 r_mcbond_other 1.985 r_angle_other_deg 1.256 r_chiral_restr 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.563 r_dihedral_angle_4_deg 19.675 r_dihedral_angle_3_deg 13.029 r_dihedral_angle_1_deg 6.248 r_mcangle_it 2.693 r_angle_refined_deg 2.083 r_mcbond_it 1.987 r_mcbond_other 1.985 r_angle_other_deg 1.256 r_chiral_restr 0.171 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3066 Nucleic Acid Atoms Solvent Atoms 190 Heterogen Atoms 84
Software Software Software Name Purpose MOLREP phasing PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling REFMAC refinement XDS data scaling