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Crystal Structure of the Chaperonin GroEL apical domain from Bordetella pertussis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P48210-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 JCSG+ D12: 0.04M Potassium phosphate monobasic, 16% PEG 6000. plate 20567 D12 drop 1, Puck: PSL-1601, Cryo: 80% crystallant + 20% glycerol
Crystal Properties Matthews coefficient Solvent content 5.08 75.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.768 α = 90 b = 145.768 β = 90 c = 34.858 γ = 120
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 EIGER2 XE 9M 2026-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 19-ID 0.9786 NSLS-II 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.95 47.71 99.9 0.177 0.182 0.041 0.999 15.3 20.2 9287
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.95 3.13 99.9 2.224 2.278 0.49 0.886 21.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.95 47.71 1.34 9243 471 99.6 0.2148 0.2129 0.2139 0.249 0.2494
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 21.671 f_angle_d 0.788 f_chiral_restr 0.048 f_bond_d 0.006 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing PDB_EXTRACT data extraction