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Crystal structure of the substrate binding domain of E. coli DnaK in complex with a short pyrrhocoricin-derived inhibitor peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DKX PDB entry 1dkx
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 2.4 M ammonium sulfate, 100 mM citric acid, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.77 55.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.579 α = 90 b = 159.965 β = 90 c = 44.931 γ = 90
Symmetry Space Group P 21 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 2007-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.0 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 2.1 69.843 98.3 0.09 0.09 7.1 3.4 32942
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.21 97.9 0.318 0.318 2.3 3.4 4705
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT PDB entry 1dkx 2.1 15 32829 1670 98.01 0.182 0.178 0.1836 0.241 0.2427 RANDOM 22.094
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] -0.86 0.53 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 14.63 r_dihedral_angle_1_deg 5.93 r_scangle_it 4.262 r_scbond_it 2.435 r_angle_other_deg 1.482 r_angle_refined_deg 1.434 r_mcangle_it 1.255 r_mcbond_it 0.644
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.859 r_dihedral_angle_4_deg 19.202 r_dihedral_angle_3_deg 14.63 r_dihedral_angle_1_deg 5.93 r_scangle_it 4.262 r_scbond_it 2.435 r_angle_other_deg 1.482 r_angle_refined_deg 1.434 r_mcangle_it 1.255 r_mcbond_it 0.644 r_mcbond_other 0.15 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3507 Nucleic Acid Atoms Solvent Atoms 496 Heterogen Atoms 30
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing