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Ensemble refinement of the crystal structure of an EF-hand protein from Danio rerio Dr.36843
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BE4 PDB entry 2BE4
Crystallization Crystal Properties Matthews coefficient Solvent content 2.3 46.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.884 α = 90 b = 52.748 β = 90 c = 114.364 γ = 90
Symmetry Space Group P 21 21 21
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 2BE4 2.1 44.17 17332 885 98.7 0.154 0.154 0.1861 0.242 0.2765 RANDOM 33.5
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] 4.53 -4 -0.53
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.6 c_scangle_it 2.81 c_mcangle_it 2.26 c_scbond_it 2.08 c_mcbond_it 1.52 c_angle_deg 1.4 c_improper_angle_d 0.93 c_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2203 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms
Software Software Software Name Purpose CNS refinement PDB_EXTRACT data extraction CNS phasing