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Ensemble refinement of the protein crystal structure of selenomethionyl gene product from Arabidopsis thaliana At5g02240 in space group P21212
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YBM PDB entry 1YBM
Crystallization Crystal Properties Matthews coefficient Solvent content 2.5 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.634 α = 90 b = 77.286 β = 90 c = 92.864 γ = 90
Symmetry Space Group P 21 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 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 1YBM 2.096 29.087 29771 1519 92.9 0.18 0.18 0.1912 0.257 0.2688 RANDOM 37.8
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 23.1 c_scangle_it 3.9 c_angle_deg 2.9 c_mcangle_it 2.66 c_scbond_it 2.65 c_improper_angle_d 2.19 c_mcbond_it 1.71 c_bond_d 0.035
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3672 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 96
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing