8X5K

The Crystal Structure of SYK from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XBB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Li2SO4, 0.1M Bis-Tris pH6.5, 25% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.095	α = 90
b = 83.903	β = 101.519
c = 39.962	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	100	PIXEL	DECTRIS EIGER X 9M		2023-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95373	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.8	41.951	99.9	0.069	12.8	5.7		22844

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84			0.763

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.8	41.951	22820	1118	99.886	0.192	0.1894	0.244	32.56

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]
2.903		-1.396	-1.725		-0.562

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.749
r_dihedral_angle_4_deg	16.209
r_dihedral_angle_3_deg	13.759
r_dihedral_angle_1_deg	6.09
r_lrange_it	5.222
r_lrange_other	5.197
r_scangle_it	3.558
r_scangle_other	3.557
r_mcangle_it	2.901
r_mcangle_other	2.9
r_scbond_it	2.213
r_scbond_other	2.212
r_mcbond_it	1.889
r_mcbond_other	1.889
r_angle_refined_deg	1.274
r_angle_other_deg	1.217
r_symmetry_xyhbond_nbd_refined	0.202
r_nbd_refined	0.189
r_symmetry_nbd_other	0.166
r_nbtor_refined	0.165
r_nbd_other	0.163
r_xyhbond_nbd_refined	0.158
r_symmetry_nbd_refined	0.122
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.058
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.005
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	2144
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing