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Ensemble refinement of the protein crystal structure of a cytosolic 5'-nucleotidase III from Mus musculus Mm.158936
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BDU PDB entry 2BDU
Crystallization Crystal Properties Matthews coefficient Solvent content 3 58.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.674 α = 90 b = 133.674 β = 90 c = 38.889 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray M SINGLE WAVELENGTH
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 Re-refinement using ensemble model THROUGHOUT PDB entry 2BDU 2.35 43.755 31910 1619 98.4 0.173 0.173 0.1873 0.243 0.2521 RANDOM 41.7
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.9 c_scangle_it 2.54 c_mcangle_it 1.96 c_scbond_it 1.89 c_mcbond_it 1.26 c_angle_deg 1.2 c_improper_angle_d 0.8 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4652 Nucleic Acid Atoms Solvent Atoms 359 Heterogen Atoms 30
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing