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Crystal structure of group III chaperonin in the open state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X9V 5X9V,3KFE experimental model PDB 3KFE 5X9V,3KFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 295 3 mM ADP, 200 mM NH4Cl, 10mM MgCl2, 50mM HEPES sodium (pH 7.0), 5% w/v Polyethylene glycol PEG 8000, 3% 1,8-Diaminooctane
Crystal Properties Matthews coefficient Solvent content 4.12 70.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 209.78 α = 90 b = 209.78 β = 90 c = 169.813 γ = 90
Symmetry Space Group P 4 21 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 PIXEL DECTRIS PILATUS 2M 2015-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.10000 Photon Factory BL-1A
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 4 50 99.7 8.4 20.3 32570
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 5X9V,3KFE 4.001 49.446 1.33 32468 1647 99.65 0.2563 0.2529 0.2607 0.321 0.324
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 15.115 f_angle_d 1.029 f_chiral_restr 0.038 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14665 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 108
Software Software Software Name Purpose PHENIX refinement XDS data processing Coot model building