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Ensemble refinement of the protein crystal structure of glyoxalase II from Arabidopsis thaliana gene At2g31350
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XM8
Crystallization Crystal Properties Matthews coefficient Solvent content 2.32 47.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.494 α = 90 b = 58.782 β = 109.22 c = 69.049 γ = 90
Symmetry Space Group P 1 21 1
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 1xm8 1.742 32.97 51925 2630 97.5 0.147 0.147 0.1476 0.193 0.1892 RANDOM 15.1
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] -0.02 0.39 -0.11 0.13
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.4 c_scangle_it 3.84 c_scbond_it 2.7 c_angle_deg 1.9 c_mcangle_it 1.56 c_improper_angle_d 1.24 c_mcbond_it 1.06 c_bond_d 0.022
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3956 Nucleic Acid Atoms Solvent Atoms 547 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing