3H9F

Crystal Structure of Human Dual Specificity Protein Kinase (TTK) in complex with a pyrimido-diazepin ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CEK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	277	25% PEG3350, 0.2M MgCl2, 0.1M BT pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.69	α = 90
b = 110.75	β = 90
c = 115.2	γ = 90

Symmetry
Space Group	I 2 2 2

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	ADSC QUANTUM 315		2009-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9782	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.6	41.414	99.7	0.061	0.061	14.4	3.9	14244	14201			80.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.74	100		0.733	0.417	2	4	2042

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3CEK	2.6	41	14267	14199	709	99.52	0.21	0.21	0.207	0.253	RANDOM	35.521

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]
-2.51			2.32		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.31
r_dihedral_angle_4_deg	25.664
r_dihedral_angle_3_deg	16.589
r_scangle_it	12.84
r_scbond_it	10.141
r_mcangle_it	6.104
r_dihedral_angle_1_deg	5.681
r_mcbond_it	3.752
r_angle_refined_deg	1.471
r_angle_other_deg	1.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.31
r_dihedral_angle_4_deg	25.664
r_dihedral_angle_3_deg	16.589
r_scangle_it	12.84
r_scbond_it	10.141
r_mcangle_it	6.104
r_dihedral_angle_1_deg	5.681
r_mcbond_it	3.752
r_angle_refined_deg	1.471
r_angle_other_deg	1.359
r_mcbond_other	0.919
r_chiral_restr	0.079
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2084
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	36

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.