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Crystal structure of encapsulated ferritin domain from Pyrococcus furiosus PFC_05175
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 0.2 M lithium chloride
20 % (w/v) PEG3350
Drops:100 nl protein, 100 nl reservoir solution. Reservoir: 70 ul.
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.853 α = 90 b = 110.057 β = 91.22 c = 136.271 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 100 PIXEL DECTRIS PILATUS 6M 2015-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.74 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.026 47.19 99.7 0.07968 0.0953 0.995 10.48 3.3 374905 22.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.026 2.099 99 0.3627 0.4412 0.902 4.02 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 MOLECULAR REPLACEMENT FREE R-VALUE 5DA5 2.026 47.19 1.34 365595 17934 96.96 0.1652 0.1741 0.1739 0.2018 0.2013 Random Selection
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 f_dihedral_angle_d 17.026 f_angle_d 0.435 f_chiral_restr 0.036 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23400 Nucleic Acid Atoms Solvent Atoms 2014 Heterogen Atoms 30
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing