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Crystal structure of group III chaperonin in the Closed state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 295 3 mM AMP-PNP, 20 mM MgCl2, 100 mM HEPES NaOH (pH 7.5), 22% Polyacrylic Acid 5100
Crystal Properties Matthews coefficient Solvent content 3.07 59.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 186.166 α = 90 b = 186.166 β = 90 c = 160.742 γ = 90
Symmetry Space Group P 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2014-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 3 50 99.1 24.7 14.9 56297
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3KFE 3.003 45.152 1.51 56286 2000 98.99 0.2007 0.1985 0.204 0.2582 0.2603
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 15.377 f_angle_d 1.22 f_chiral_restr 0.062 f_bond_d 0.015 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14652 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose PHENIX refinement HKL-2000 data processing HKL-2000 data scaling Coot model building