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Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide EANQQKPLLGLFADG
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 7 293 2.8 M (NH4)2SO4, 0.1 M K3PO4
Crystal Properties Matthews coefficient Solvent content 2.08 40.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.621 α = 90 b = 95.607 β = 90 c = 117.614 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 PILATUS3 R 200K-A Rigaku VariMax HF 2020-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.39 50 98.9 0.166 0.186 0.08 8.7 4.9 8602
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 2.39 2.43 92.3 2.182 2.581 1.339 0.332 3.2
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 MOLECULAR REPLACEMENT THROUGHOUT 1DKZ 2.4 47.85 8145 409 98.19 0.2597 0.2556 0.2554 0.3323 0.3283 RANDOM 53.306
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] 0.96 1.63 -2.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.751 r_dihedral_angle_3_deg 18.299 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_1_deg 6.976 r_angle_refined_deg 1.407 r_angle_other_deg 1.188 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.751 r_dihedral_angle_3_deg 18.299 r_dihedral_angle_4_deg 16.866 r_dihedral_angle_1_deg 6.976 r_angle_refined_deg 1.407 r_angle_other_deg 1.188 r_chiral_restr 0.049 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1611 Nucleic Acid Atoms Solvent Atoms 23 Heterogen Atoms 22
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction