3H80

Crystal structure of the amino-terminal domain of HSP90 from Leishmania major, LmjF33.0312:M1-K213


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3EKOPDB entry 3EKO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529325% PEG 3350, 0.1 M Ammonium sulfate, 0.1 M Bis-Tris pH 5.5, 2 mM AMPPNP, 4 mM MgCl2, 2 mM TCEP, 25% Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5651.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.431α = 90
b = 43.197β = 90
c = 50.502γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-04-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.96863APS23-ID-B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.985094.60.0720.06434.5886.2181691816921.192
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.0169.60.20.2155.423.1650

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB entry 3EKO246.68170131701393395.30.197620.197620.193710.27289RANDOM27.215
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]
-0.24-0.20.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.941
r_dihedral_angle_4_deg17.019
r_dihedral_angle_3_deg16.041
r_dihedral_angle_1_deg6.164
r_scangle_it4.281
r_scbond_it2.642
r_mcangle_it1.848
r_angle_refined_deg1.579
r_mcbond_it1.187
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.941
r_dihedral_angle_4_deg17.019
r_dihedral_angle_3_deg16.041
r_dihedral_angle_1_deg6.164
r_scangle_it4.281
r_scbond_it2.642
r_mcangle_it1.848
r_angle_refined_deg1.579
r_mcbond_it1.187
r_nbtor_refined0.299
r_xyhbond_nbd_refined0.224
r_symmetry_vdw_refined0.221
r_nbd_refined0.2
r_symmetry_hbond_refined0.132
r_chiral_restr0.092
r_bond_refined_d0.015
r_metal_ion_refined0.014
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 Atoms1671
Nucleic Acid Atoms
Solvent Atoms157
Heterogen Atoms61

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling