2YEF

HSP90 inhibitors and drugs from fragment and virtual screening


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WI1PDB ENTRY 2WI1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.0339.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.023α = 90
b = 44.25β = 115.79
c = 53.699γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU R-AXIS IVOSMIC BLUE MIRRORS2002-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

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
11.5548.7994.20.02122.5298532
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)
11.551.5961.50.59

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 2WI11.5548.7929853157794.250.178110.175930.21878RANDOM18.515
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]
-0.17-0.330.06-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.022
r_dihedral_angle_4_deg21.172
r_dihedral_angle_3_deg13.292
r_dihedral_angle_1_deg6.81
r_scangle_it6.092
r_scbond_it3.89
r_mcangle_it2.449
r_angle_refined_deg2.294
r_mcbond_it1.485
r_chiral_restr0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.022
r_dihedral_angle_4_deg21.172
r_dihedral_angle_3_deg13.292
r_dihedral_angle_1_deg6.81
r_scangle_it6.092
r_scbond_it3.89
r_mcangle_it2.449
r_angle_refined_deg2.294
r_mcbond_it1.485
r_chiral_restr0.16
r_bond_refined_d0.027
r_gen_planes_refined0.013
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_other
r_long_range_B_refined
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 Atoms1706
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing