7F4X

Joint neutron and X-ray crystal structure of the nucleotide-binding domain of Hsp72 in complex with ADP


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AQZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29320-25% PEG 2000 MME, 90 mMsodium acetate, 10 mM acetic acid, 200 mM MgCl2, 10%(v/v) glycerol
Crystal Properties
Matthews coefficientSolvent content
2.6353.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.677α = 90
b = 64.618β = 90
c = 145.593γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298PIXELDECTRIS PILATUS 12M2017-05-14MSINGLE WAVELENGTH
21neutron298IMAGE PLATEMAATEL IMAGINE2017-06-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.00Photon FactoryAR-NW12A
2NUCLEAR REACTORFRM II BEAMLINE BIODIFF3.98FRM IIBIODIFF

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
11.644.4597.50.08113.55.757639
22.239.390.40.1178.12.320952
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.660.7332.45.9
22.22.260.3742.92.1

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT1.637.8381.3757604288197.560.16670.16550.1898
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.19938.80520935105390.420.1860.18410.222
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d16.309
f_dihedral_angle_d16.309
f_angle_d0.992
f_angle_d0.992
f_chiral_restr0.074
f_chiral_restr0.074
f_bond_d0.007
f_bond_d0.007
f_plane_restr0.005
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2930
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms29

Software

Software
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing