7UP5 | pdb_00007up5

Crystal structure of C-terminal Domain of MSK1 in complex with covalently bound pyrrolopyrimidine compound 23 (co-crystal)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		in-house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	The protein (10.1 mg/ml) was exchanged into 25 mM HEPES pH 7.5, 150 mM NaCl, 5% glycerol, 1 mM DTT using a GE (GE28-9180-04) spin column according to manufacturer's instructions. The protein was then diluted to 0.5 mg/ml in the same buffer and incubated with 150 micromolar UCB170414/BSI108592 for an hour on ice (~10 fold)and concentrated back down to 5 mg/ml. Crystals were produced by sitting drop vapor diffusion with an equal volume of the protein, Msk1-C terminal domain (PID7059-1, CID101276) and a crystallization buffer containing 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD: 30mM of each sodium fluoride/iodide/bromide: 100 mM Na HEPES/MOPS pH 8.5 (tray ID 303042, well B12, Morpheus). Crystals were directly vitrified in in liquid N2. Puck ID QRL9-2

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.48	α = 90
b = 90.78	β = 90
c = 135.97	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	0.99999	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.8	50	100	0.123	0.134	0.997	13.83	6.495		16319			44.306

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.87	100		0.616	0.668	0.851	3.24	6.691

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	FREE R-VALUE	in-house model	2.8	48.145	1.34	16314	1696	99.95	0.2077	0.2008	0.2	0.2678	0.27	0	50.6763

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4220
Nucleic Acid Atoms
Solvent Atoms	38
Heterogen Atoms	37

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing
Coot	model building

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.