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Crystal structure of the substrate binding domain of E. coli DnaK in complex with a long pyrrhocoricin-derived inhibitor peptide (form A)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DPO PDB entry 3dpo
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 2.64 53.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.87 α = 90 b = 159.12 β = 90 c = 44.79 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 293 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 15 87.7 0.217 3.8 46703 17463
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.59 93 0.371 1.8
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 3dpo 2.5 15 17451 892 87.79 0.241 0.237 0.2347 0.316 0.3137 RANDOM 42.361
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] -2.4 1.26 1.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.713 r_dihedral_angle_4_deg 21.204 r_dihedral_angle_3_deg 18.152 r_dihedral_angle_1_deg 7.854 r_scangle_it 3.565 r_mcangle_it 2.841 r_scbond_it 2.342 r_angle_other_deg 2.049 r_angle_refined_deg 2.041 r_mcbond_it 1.856
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.713 r_dihedral_angle_4_deg 21.204 r_dihedral_angle_3_deg 18.152 r_dihedral_angle_1_deg 7.854 r_scangle_it 3.565 r_mcangle_it 2.841 r_scbond_it 2.342 r_angle_other_deg 2.049 r_angle_refined_deg 2.041 r_mcbond_it 1.856 r_mcbond_other 0.505 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3434 Nucleic Acid Atoms Solvent Atoms 309 Heterogen Atoms 5
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data reduction