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Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At2g37210
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2A33 PDB entry 2A33
Crystallization Crystal Properties Matthews coefficient Solvent content 1.9 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.403 α = 90 b = 66.773 β = 90 c = 98.639 γ = 90
Symmetry Space Group P 21 21 21
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 2A33 1.95 46.96 26352 1336 99.7 0.168 0.168 0.1817 0.224 0.2306 RANDOM 25.7
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] -0.76 -0.29 1.05
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.6 c_scangle_it 3.63 c_scbond_it 2.55 c_mcangle_it 2.06 c_mcbond_it 1.52 c_angle_deg 1.5 c_improper_angle_d 0.99 c_bond_d 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2636 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 11
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing