3ATU

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2E8APDB ENTRY 2E8A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1M HEPES-NaOH (pH 7.0), 0.15M MgCl2, 30 % PEG MME 500, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4449.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.114α = 90
b = 63.675β = 90
c = 143.534γ = 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 BL26B21SPring-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
11.655098.10.05928.86.250891
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)
11.651.7185.70.3742.4

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 2E8A1.652048203258698.180.187460.185860.21781RANDOM22.953
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]
0.60.23-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.019
r_dihedral_angle_4_deg19.078
r_dihedral_angle_3_deg12.465
r_dihedral_angle_1_deg5.155
r_scangle_it3.387
r_scbond_it2.084
r_mcangle_it1.347
r_angle_refined_deg1.334
r_mcbond_it0.741
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.019
r_dihedral_angle_4_deg19.078
r_dihedral_angle_3_deg12.465
r_dihedral_angle_1_deg5.155
r_scangle_it3.387
r_scbond_it2.084
r_mcangle_it1.347
r_angle_refined_deg1.334
r_mcbond_it0.741
r_nbtor_refined0.302
r_nbd_refined0.202
r_symmetry_vdw_refined0.186
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.136
r_chiral_restr0.09
r_metal_ion_refined0.083
r_bond_refined_d0.011
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2938
Nucleic Acid Atoms
Solvent Atoms368
Heterogen Atoms42

Software

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