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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 B)
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 2.62 53.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.712 α = 90 b = 91.653 β = 90 c = 154.797 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.0 ESRF ID14-4
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 1.8 19.893 86.7 0.076 0.076 6.7 5.4 27880
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) 1.95 2.06 90.4 0.342 0.342 2.1 5.1 10524
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 2.6 8 27432 1354 82.05 0.257 0.254 0.2662 0.319 0.273 RANDOM 24.921
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] -1.69 1.81 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.137 r_dihedral_angle_3_deg 19.769 r_dihedral_angle_4_deg 17.979 r_dihedral_angle_1_deg 7.248 r_scangle_it 5.307 r_mcangle_it 5.055 r_scbond_it 3.782 r_mcbond_it 3.6 r_angle_other_deg 1.971 r_angle_refined_deg 1.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.137 r_dihedral_angle_3_deg 19.769 r_dihedral_angle_4_deg 17.979 r_dihedral_angle_1_deg 7.248 r_scangle_it 5.307 r_mcangle_it 5.055 r_scbond_it 3.782 r_mcbond_it 3.6 r_angle_other_deg 1.971 r_angle_refined_deg 1.824 r_mcbond_other 0.988 r_chiral_restr 0.103 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6960 Nucleic Acid Atoms Solvent Atoms 1466 Heterogen Atoms 5
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing