8HJE

Vismodegib binds to the catalytical domain of human Ubiquitin-Specific Protease 28


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6HEHPDB code 6HEH was used as a strating search model.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.42910.1 M Bis-tris propane pH 6.4, 0.2 M potassium thiocyanate, 20% PEG3350 and 3% sucrose
Crystal Properties
Matthews coefficientSolvent content
2.2368.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.099α = 90
b = 105.099β = 90
c = 327.422γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS EIGER X 9M2021-07-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL02U10.9792SSRFBL02U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.8543.8599.580.99920.76216695
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.8512.9530.902

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.8543.851588182599.960.223720.222060.25429RANDOM66.552
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]
1.580.791.58-5.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.525
r_dihedral_angle_4_deg22.167
r_dihedral_angle_3_deg18.127
r_long_range_B_refined11.998
r_long_range_B_other11.996
r_scangle_other9.607
r_mcangle_other8.846
r_mcangle_it8.843
r_dihedral_angle_1_deg7.946
r_scbond_it6.658
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.525
r_dihedral_angle_4_deg22.167
r_dihedral_angle_3_deg18.127
r_long_range_B_refined11.998
r_long_range_B_other11.996
r_scangle_other9.607
r_mcangle_other8.846
r_mcangle_it8.843
r_dihedral_angle_1_deg7.946
r_scbond_it6.658
r_scbond_other6.656
r_mcbond_it6.184
r_mcbond_other6.166
r_angle_refined_deg1.597
r_angle_other_deg1.255
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2411
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
xia2data scaling
xia2data reduction
REFMACphasing