☰ Navigation Tabs
Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the peptide QEHTGSQLRIAAYGP
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 2.4 M (NH4)2SO4, 0.1 M K3PO4
Crystal Properties Matthews coefficient Solvent content 2.05 39.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.269 α = 90 b = 95.61 β = 90 c = 116.98 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 2019-08-05 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 2.4 50 99.4 0.152 0.167 0.09 5.2 4.2 8444
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 97.8 0.714 0.615 3.8
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 MOLECULAR REPLACEMENT THROUGHOUT 1DKZ 2.4 30.77 8036 404 99.03 0.2271 0.2238 0.2266 0.2864 0.2874 RANDOM 32.888
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] 1.77 0.58 -2.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.056 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 17.515 r_dihedral_angle_1_deg 7.307 r_angle_refined_deg 1.446 r_angle_other_deg 1.229 r_chiral_restr 0.052 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.056 r_dihedral_angle_4_deg 22.89 r_dihedral_angle_3_deg 17.515 r_dihedral_angle_1_deg 7.307 r_angle_refined_deg 1.446 r_angle_other_deg 1.229 r_chiral_restr 0.052 r_bond_refined_d 0.006 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 1643 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 10
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing