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Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At5g08170, agmatine iminohydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKP PDB entry 1VKP
Crystallization Crystal Properties Matthews coefficient Solvent content 2.55 51.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.02 α = 90 b = 115.813 β = 97.1 c = 66.634 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 PDB entry 1VKP 1.53 19.87 119958 6038 91.8 0.135 0.135 0.1393 0.171 0.1718 RANDOM 18.3
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 24.6 c_scangle_it 3.53 c_angle_deg 2.7 c_scbond_it 2.5 c_mcangle_it 2.03 c_improper_angle_d 1.97 c_mcbond_it 1.41 c_bond_d 0.036
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5784 Nucleic Acid Atoms Solvent Atoms 779 Heterogen Atoms 67
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing