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Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide RALALLPLSR
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 6.9 293 2.6 M (NH4)2SO4, 0.1 M K3PO4
Crystal Properties Matthews coefficient Solvent content 2.1 41.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.763 α = 90 b = 94.773 β = 90 c = 117.109 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 2019-09-10 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 2.54 50 96.6 0.161 0.185 0.117 4 3.1 6943
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 2.54 2.58 89.9 0.307 2.7
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 2.55 30.52 6606 336 96.63 0.2128 0.2082 0.2143 0.3065 0.3145 RANDOM 44.083
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] 2.88 -0.03 -2.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.762 r_dihedral_angle_4_deg 23.37 r_dihedral_angle_3_deg 19.721 r_dihedral_angle_1_deg 7.478 r_angle_refined_deg 1.563 r_angle_other_deg 1.216 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.762 r_dihedral_angle_4_deg 23.37 r_dihedral_angle_3_deg 19.721 r_dihedral_angle_1_deg 7.478 r_angle_refined_deg 1.563 r_angle_other_deg 1.216 r_chiral_restr 0.055 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1633 Nucleic Acid Atoms Solvent Atoms 13 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing PDB_EXTRACT data extraction