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Crystal structure of the molecular chaperone DnaK from Geobacillus kaustophilus HTA426 in post-ATP hydrolysis state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HSC PDB ENTRY 3HSC, 1DKZ experimental model PDB 1DKZ PDB ENTRY 3HSC, 1DKZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 200 MM AMMONIUM CITRATE, PH 7.5, 20% (V/V) ISOPROPANOL, 15% (W/V) PEG3350
Crystal Properties Matthews coefficient Solvent content 3.15 61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.753 α = 90 b = 71.455 β = 90 c = 183.864 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 100 CCD ADSC CCD VERTICALLY COLLIMATING PREMIRROR, LN2-COOLED FIXED-EXIT DOUBLE CRYSTAL SI(111) MONOCHROMATOR , TOROIDAL FOCUSING MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
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 2.37 29.58 94.8 0.06 14.9 3.1 25994 2 30.2
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) 1 2.37 2.45 93.9 0.49 2 3.1
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 PDB ENTRY 3HSC, 1DKZ 2.37 29.58 25994 1251 89.3 0.227 0.227 0.2226 0.27 0.2637 RANDOM 43.8
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] -3.78 5.04 -1.26
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_scangle_it 6.86 c_scbond_it 5.43 c_mcangle_it 4.56 c_improper_angle_d 4.22 c_mcbond_it 3.17 c_angle_deg 2.4 c_bond_d 0.014 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.5 c_scangle_it 6.86 c_scbond_it 5.43 c_mcangle_it 4.56 c_improper_angle_d 4.22 c_mcbond_it 3.17 c_angle_deg 2.4 c_bond_d 0.014 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3720 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 33
Software Software Software Name Purpose CNS refinement Blu-Ice data reduction SCALEPACK data scaling MOLREP phasing