3AY9

Crystal structure of human Hsp70 NBD in the ADP-, Mg ion-, and K ion-bound state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ATUPDB ENTRY 3ATU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.72930.05M calcium chloride, 0.1M bis-tris (pH6.5), 30% PEG MME 550, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3246.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.733α = 90
b = 61.343β = 90
c = 142.65γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHmirrorsMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.54SPring-8BL26B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.755092.50.12910.13496.2184236093
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8187.70.5233.60131

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3ATU1.752036093191492.140.19020.188960.21275RANDOM26.317
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]
-0.983.37-2.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg18.491
r_dihedral_angle_3_deg13.203
r_dihedral_angle_1_deg5.363
r_scangle_it4.198
r_scbond_it2.508
r_mcangle_it1.475
r_angle_refined_deg1.412
r_mcbond_it0.793
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.032
r_dihedral_angle_4_deg18.491
r_dihedral_angle_3_deg13.203
r_dihedral_angle_1_deg5.363
r_scangle_it4.198
r_scbond_it2.508
r_mcangle_it1.475
r_angle_refined_deg1.412
r_mcbond_it0.793
r_nbtor_refined0.305
r_nbd_refined0.204
r_metal_ion_refined0.2
r_symmetry_vdw_refined0.158
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.128
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms266
Heterogen Atoms36

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling