3HYY

Crystal structure of Hsp90 with fragment 37-D04


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherin-house Hsp90 model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52770.2M Magnesium chloride, 0.1M Sodium cacodylate, 19-23% PEG2000 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6854.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.936α = 90
b = 90.604β = 90
c = 98.765γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.542

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.966.8990.069.92.662381824.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9596.20.332.44

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 REPLACEMENTTHROUGHOUTin-house Hsp90 model1.924.7522586120898.890.193810.19150.23784RANDOM24.375
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]
-0.40.320.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg22.423
r_dihedral_angle_3_deg14.427
r_dihedral_angle_1_deg6.44
r_scangle_it5.843
r_scbond_it3.694
r_mcangle_it2.248
r_angle_refined_deg2.105
r_mcbond_it1.275
r_chiral_restr0.144
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.772
r_dihedral_angle_4_deg22.423
r_dihedral_angle_3_deg14.427
r_dihedral_angle_1_deg6.44
r_scangle_it5.843
r_scbond_it3.694
r_mcangle_it2.248
r_angle_refined_deg2.105
r_mcbond_it1.275
r_chiral_restr0.144
r_bond_refined_d0.024
r_gen_planes_refined0.009
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1635
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms15

Software

Software
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling