Experiment: 5VCX

CRYSTAL STRUCTURE OF HUMAN MYT1 KINASE DOMAIN (UNTREATED) IN COMPLEX WITH SARACATINIB

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5VCV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	6.9 MG/ML MYT1, 25 mM HEPES, 100 MM SODIUM CHLORIDE, 0.5 mM DTT, 0.1 M CALCIUM CHLORIDE, 0.05 M TRIS pH 8.5, 10 % PEG 4000, 1 mM SARACATINIB

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.48	α = 90
b = 69.43	β = 90
c = 86.53	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	CCD	MARMOSAIC 225 mm CCD		2013-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.00	APS	22-BM

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	2.7	43.814	99.2	0.047	0.052	0.999	27.81	5.655		9718		-3	49.5

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	2.7	2.77	99.9		0.328	0.361	0.938	4.84	5.767

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5VCV	2.7	43.814	1.37	9718	486	99.19	0.2013	0.2067	0.2436	0.2467	54.6016

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	16.616
f_angle_d	1.162
f_chiral_restr	0.032
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2230
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	42

Software

Software
Software Name	Purpose
XSCALE	data scaling
SERGUI	data collection
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing