2BSM

Novel, potent small molecule inhibitors of the molecular chaperone Hsp90 discovered through structure-based design


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UY6PDB ENTRY 1UY6

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.525% PEG MME 2000, 0.1M NA CACODYLATE, PH6.5, 0.2M MGCL2., pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.856

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 65.398α = 90
b = 88.841β = 90
c = 99.273γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC BLUE MIRRORS2003-01-06MSINGLE 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
12.053098.50.086.42.1185122
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)
12.052.1293.10.371.61.7

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1UY62.05301737193498.90.1950.1920.244RANDOM33.8
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]
-0.280.72-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.275
r_scangle_it3.163
r_scbond_it1.863
r_angle_refined_deg1.395
r_mcangle_it1.357
r_angle_other_deg0.82
r_mcbond_it0.726
r_symmetry_vdw_other0.237
r_nbd_other0.236
r_symmetry_hbond_refined0.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.275
r_scangle_it3.163
r_scbond_it1.863
r_angle_refined_deg1.395
r_mcangle_it1.357
r_angle_other_deg0.82
r_mcbond_it0.726
r_symmetry_vdw_other0.237
r_nbd_other0.236
r_symmetry_hbond_refined0.218
r_xyhbond_nbd_refined0.21
r_nbd_refined0.189
r_nbtor_other0.083
r_chiral_restr0.078
r_symmetry_vdw_refined0.05
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms1628
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms27

Software

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