2V7Y | pdb_00002v7y

Crystal structure of the molecular chaperone DnaK from Geobacillus kaustophilus HTA426 in post-ATP hydrolysis state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3HSCPDB ENTRY 3HSC, 1DKZ
experimental modelPDB 1DKZPDB ENTRY 3HSC, 1DKZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5200 MM AMMONIUM CITRATE, PH 7.5, 20% (V/V) ISOPROPANOL, 15% (W/V) PEG3350
Crystal Properties
Matthews coefficientSolvent content
3.1561

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.753α = 90
b = 71.455β = 90
c = 183.864γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDVERTICALLY COLLIMATING PREMIRROR, LN2-COOLED FIXED-EXIT DOUBLE CRYSTAL SI(111) MONOCHROMATOR , TOROIDAL FOCUSING MIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B1NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.3729.5894.80.0614.93.125994230.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.372.4593.90.4923.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3HSC, 1DKZ2.3729.5825994125189.30.2270.2270.220.270.26RANDOM43.8
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]
-3.785.04-1.26
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.5
c_scangle_it6.86
c_scbond_it5.43
c_mcangle_it4.56
c_improper_angle_d4.22
c_mcbond_it3.17
c_angle_deg2.4
c_bond_d0.014
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d26.5
c_scangle_it6.86
c_scbond_it5.43
c_mcangle_it4.56
c_improper_angle_d4.22
c_mcbond_it3.17
c_angle_deg2.4
c_bond_d0.014
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 AtomsNumber
Protein Atoms3720
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms33

Software

Software
Software NamePurpose
CNSrefinement
Blu-Icedata reduction
SCALEPACKdata scaling
MOLREPphasing