6GPT

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


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 AMPCP, 500 mM NaCl, 20 mM TRIS, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
238.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.861α = 90
b = 43.935β = 116.17
c = 54.29γ = 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 I030.97662DiamondI03

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
1248.7299.30.0950.1130.060.91110.13.715496214.2
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)
122.1199.70.280.3270.1670.8875.83.7

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 REPLACEMENTTHROUGHOUT2XK2248.381467079399.190.177770.17460.23211RANDOM22.407
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]
-0.11-0.020.030.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.354
r_dihedral_angle_4_deg25.89
r_dihedral_angle_3_deg14.358
r_long_range_B_refined7.295
r_dihedral_angle_1_deg7.001
r_angle_refined_deg2.035
r_mcangle_it1.873
r_scbond_it1.79
r_mcbond_it1.185
r_chiral_restr0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.354
r_dihedral_angle_4_deg25.89
r_dihedral_angle_3_deg14.358
r_long_range_B_refined7.295
r_dihedral_angle_1_deg7.001
r_angle_refined_deg2.035
r_mcangle_it1.873
r_scbond_it1.79
r_mcbond_it1.185
r_chiral_restr0.124
r_gen_planes_refined0.013
r_bond_refined_d0.012
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 Atoms1674
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing