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Ensemble refinement of the crystal structure of a lysine decarboxylase-like protein from Arabidopsis thaliana gene At5g11950
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YDH PDB entry 1YDH
Crystallization Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.589 α = 90 b = 80.427 β = 102.97 c = 50.709 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray APS-1 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 1YDH 2.152 34.35 25678 1300 99 0.152 0.152 0.1688 0.207 0.2229 RANDOM 26.5
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] 1.08 1.17 -1.07
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 21.3 c_scangle_it 2.57 c_scbond_it 1.96 c_mcangle_it 1.73 c_mcbond_it 1.2 c_angle_deg 1.1 c_improper_angle_d 0.83 c_bond_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2796 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 20
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing