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Ensemble refinement of the crystal structure of a glycolipid transfer-like protein from Galdieria sulphuraria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I3F PDB entry 2I3F
Crystallization Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.438 α = 90 b = 48.195 β = 115.06 c = 89.411 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 PDB entry 2I3F 1.38 41.99 93170 4669 98.8 0.166 0.166 0.1648 0.202 0.2003 RANDOM 16.7
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] -0.66 1.04 -0.25 0.91
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 19.3 c_scangle_it 3.11 c_scbond_it 2.24 c_angle_deg 1.8 c_mcangle_it 1.74 c_mcbond_it 1.34 c_improper_angle_d 1.24 c_bond_d 0.016
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3348 Nucleic Acid Atoms Solvent Atoms 384 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing