8RRQ | pdb_00008rrq

Crystal structure of human SYK in complex with compound 24

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
2.08	41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.204	α = 90
b = 87.344	β = 92.159
c = 40.048	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 PILATUS 6M-F	Toroidal mirror	2017-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9796	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.6	43.67	98.7	0.019	1	17.4	2		34990

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	91.9		0.318	0.823	2.2	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	1.6	43.67	34990	1746	98.513	0.178	0.1766	0.1764	0.2107	0.2107	25.887

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]
0.011		1.279	-1.001		0.891

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.455
r_dihedral_angle_3_deg	16.466
r_dihedral_angle_2_deg	12.217
r_lrange_it	7.36
r_lrange_other	7.36
r_dihedral_angle_1_deg	6.297
r_scangle_it	5.814
r_scangle_other	5.812
r_scbond_it	3.863
r_scbond_other	3.862
r_mcangle_it	3.156
r_mcangle_other	3.155
r_mcbond_it	2.348
r_mcbond_other	2.339
r_angle_refined_deg	1.748
r_chiral_restr_other	0.849
r_angle_other_deg	0.619
r_nbd_refined	0.222
r_nbd_other	0.195
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.165
r_symmetry_xyhbond_nbd_refined	0.137
r_symmetry_nbd_refined	0.127
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_symmetry_xyhbond_nbd_other	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2143
Nucleic Acid Atoms
Solvent Atoms	178
Heterogen Atoms	37

Software

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