6GPR

Structure of human Heat shock protein 90-alpha N-terminal domain (Hsp90-NTD) in complex with cAMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XK2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291Precipitant: 25 % wt/vol PEG 2000, 200mM MgCl2, 100 mM sodium cacodylate, pH 6.5 Sample: Hsp90a-NTD 20 mg/mL, 10 mM cAMP, 500 mM NaCl, 20 mM TRIS, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.4148.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.502α = 90
b = 44.346β = 115.6
c = 54.023γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2018-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97623DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.3548.7299.80.1440.170.0890.9626.63.79680214.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4899.70.340.3980.2050.8743.93.8

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 REPLACEMENTTHROUGHOUT2XK22.3548.72913551599.570.226390.223170.2858RANDOM21.603
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]
1.65-4.4711.06-5.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.048
r_dihedral_angle_4_deg28.278
r_dihedral_angle_3_deg17.845
r_dihedral_angle_1_deg8.393
r_long_range_B_refined4.68
r_mcangle_it2.337
r_angle_refined_deg1.771
r_scbond_it1.708
r_mcbond_it1.498
r_chiral_restr0.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.048
r_dihedral_angle_4_deg28.278
r_dihedral_angle_3_deg17.845
r_dihedral_angle_1_deg8.393
r_long_range_B_refined4.68
r_mcangle_it2.337
r_angle_refined_deg1.771
r_scbond_it1.708
r_mcbond_it1.498
r_chiral_restr0.171
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1642
Nucleic Acid Atoms
Solvent Atoms121
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing