9PE9 | pdb_00009pe9

GSK3beta in complex with compound 6

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Internal X-ray structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		294.15	Well volume: 100.0 uL Well Ingredients: Buffer: 0.1 M (10.0 uL of stock 1.0 M) bicine (pH 9.00) Precipitant: 14.0 %w/v (35.0 uL of stock 40.0 %w/v) PEG 10000 Plate setup temperature: 21 C Plate incubation temperature: 21 C Drop volume from well: 1.0 uL Drop protein volume: 1.0 uL Protein Formulation Composition: Protein: GSK3B (4.85 mg/mL) (0.12 mM) Compound: PF-6825089 (0.50 mM)

Crystal Properties
Matthews coefficient	Solvent content
3	59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.63	α = 90
b = 109.25	β = 100.99
c = 67.65	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS 12M		2018-02-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

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	2.11	21.21	93.77	0.999	14.92	3.4		54620

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	2.11	2.185	75.71		0.839	2.41	3.5

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	2.11	21.21	52197	2615	94.2	0.2214	0.22	0.2095	0.2473	0.2352	RANDOM	43.96

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]
-0.4098		2.3083	0.5151		-0.1053

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	16.67
t_omega_torsion	3.25
t_angle_deg	0.89
t_bond_d	0.008
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5316
Nucleic Acid Atoms
Solvent Atoms	373
Heterogen Atoms	66

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
autoBUSTER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.