3SRV

Crystal structure of spleen tyrosine kinase (SYK) in complex with a diaminopyrimidine carboxamide inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		OTHER IN-HOUSE COORDINATES

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	20% PEG3350, 0.2M Na-K-Phosphate, 0.1M Bis-Tris-Propane pH 6.5, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.124	α = 99.68
b = 42.316	β = 90.16
c = 87.621	γ = 100.19

Symmetry
Space Group	P 1

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 315r		2010-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9763	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.95	39.47	94.7	0.052	11.1	1.9	38589	38589			25.7

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	1.95	2.06	94.7		0.402	0.402	1.7	1.9	5634

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	OTHER IN-HOUSE COORDINATES	1.95	20	38566	1929	100	0.1875	0.1846	0.241	RANDOM	35.6065

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]
-0.71	-1.13	0.19	1.61	0.69	-1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.25
r_dihedral_angle_4_deg	16.99
r_dihedral_angle_3_deg	13.965
r_dihedral_angle_1_deg	4.399
r_scangle_it	4.399
r_scbond_it	2.875
r_mcangle_it	2.187
r_angle_refined_deg	1.378
r_mcbond_it	1.218
r_angle_other_deg	0.881

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.25
r_dihedral_angle_4_deg	16.99
r_dihedral_angle_3_deg	13.965
r_dihedral_angle_1_deg	4.399
r_scangle_it	4.399
r_scbond_it	2.875
r_mcangle_it	2.187
r_angle_refined_deg	1.378
r_mcbond_it	1.218
r_angle_other_deg	0.881
r_mcbond_other	0.245
r_chiral_restr	0.088
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4292
Nucleic Acid Atoms
Solvent Atoms	472
Heterogen Atoms	74

Software

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