8RRZ | pdb_00008rrz

Crystal structure of SYK kinase in complex with compound 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		in-house SYK structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	277	20% PEG 3350, 0.1 M bis tris propane pH 6.5, 0.2 M Na formate

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.085	α = 90
b = 84.859	β = 99.329
c = 40.845	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 R 4M	CRL	2018-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.75	42.43	98.6	0.025	0.034	0.025	0.999	17.7	2		26808

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	99.4		0.32	0.453	0.32	0.881		2

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.75	39.586	26808	1339	98.562	0.182	0.1802	0.1737	0.2145	0.2086	27.308

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]
-1.573		-0.698	-1.559		3.189

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.902
r_dihedral_angle_6_deg	16.684
r_dihedral_angle_2_deg	13.595
r_lrange_it	7.439
r_lrange_other	7.42
r_dihedral_angle_1_deg	6.589
r_scangle_it	6.208
r_scangle_other	6.206
r_scbond_it	4.054
r_scbond_other	4.052
r_mcangle_it	3.652
r_mcangle_other	3.651
r_mcbond_it	2.664
r_mcbond_other	2.655
r_angle_refined_deg	1.77
r_chiral_restr_other	0.819
r_angle_other_deg	0.777
r_symmetry_nbd_refined	0.373
r_nbd_other	0.286
r_nbd_refined	0.274
r_xyhbond_nbd_refined	0.215
r_symmetry_nbd_other	0.213
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.185
r_chiral_restr	0.093
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.011
r_symmetry_xyhbond_nbd_other	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2138
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	45

Software

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