☰ Navigation Tabs
Ensemble refinement of the protein crystal structure of spermidine synthase from Arabidopsis thaliana gene At1g23820
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XJ5 PDB entry 1XJ5
Crystallization Crystal Properties Matthews coefficient Solvent content 2.46 50.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.814 α = 90 b = 95.207 β = 104.96 c = 89.164 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 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 1XJ5 2.7 26.29 37779 3788 95.5 0.164 0.164 0.166 0.249 0.2448 RANDOM 37.2
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] -2.91 1.24 14.18 -11.27
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.6 c_scangle_it 5.02 c_mcangle_it 3.87 c_scbond_it 3.12 c_mcbond_it 2.19 c_angle_deg 1.3 c_improper_angle_d 0.95 c_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8864 Nucleic Acid Atoms Solvent Atoms 576 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing