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E. coli DnaK bound to peptide PA9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 0.2 M NH4F and 2.2 M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.454 α = 90 b = 94.836 β = 90 c = 116.59 γ = 90
Symmetry Space Group I 2 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 PIXEL DECTRIS EIGER X 9M 2024-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.92010 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.87 28.5 92.8 0.09 0.053 0.998 8 4.9 16389 36.47
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.9 99.7 0.434 0.7 5.2
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 1.87 26.97 1.33 15880 738 89.94 0.2421 0.2411 0.2413 0.2628 0.2626 47.45
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 8.1326 f_angle_d 1.0751 f_chiral_restr 0.0607 f_plane_restr 0.0098 f_bond_d 0.0063
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1616 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 55
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHENIX phasing