8HJE | pdb_00008hje

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6HEH	PDB code 6HEH was used as a strating search model.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.4	291	0.1 M Bis-tris propane pH 6.4, 0.2 M potassium thiocyanate, 20% PEG3350 and 3% sucrose

Crystal Properties
Matthews coefficient	Solvent content
2.23	68.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.099	α = 90
b = 105.099	β = 90
c = 327.422	γ = 120

Symmetry
Space Group	H 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS EIGER X 9M		2021-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.9792	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.85	43.85	99.58	0.999	20.76	2		16695

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.851	2.953			0.902

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.85	43.85	15881	825	99.96	0.22372	0.22206	0.24	0.25429	0.26	RANDOM	66.552

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]
1.58	0.79		1.58		-5.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.525
r_dihedral_angle_4_deg	22.167
r_dihedral_angle_3_deg	18.127
r_long_range_B_refined	11.998
r_long_range_B_other	11.996
r_scangle_other	9.607
r_mcangle_other	8.846
r_mcangle_it	8.843
r_dihedral_angle_1_deg	7.946
r_scbond_it	6.658
r_scbond_other	6.656
r_mcbond_it	6.184
r_mcbond_other	6.166
r_angle_refined_deg	1.597
r_angle_other_deg	1.255
r_chiral_restr	0.064
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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 Atoms	Number
Protein Atoms	2411
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
xia2	data reduction
REFMAC	phasing