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Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g03250, a putative UDP-glucose pyrophosphorylase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Z90
Crystallization Crystal Properties Matthews coefficient Solvent content 2.4 48.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 188.68 α = 90 b = 58.863 β = 100.4 c = 89.862 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 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 1Z90 1.863 37.365 79504 3986 97.6 0.171 0.171 0.1739 0.231 0.2318 RANDOM 25.5
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.9 c_scangle_it 2.79 c_scbond_it 2.16 c_mcangle_it 2.13 c_mcbond_it 1.53 c_angle_deg 1.5 c_improper_angle_d 1.04 c_bond_d 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7122 Nucleic Acid Atoms Solvent Atoms 421 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing