8WM0

Crystal structure of TNIK-thiopeptide wTP3 complex

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		283	13% Tacsimate pH6.0

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.72	α = 90
b = 53.72	β = 90
c = 220.17	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	PIXEL	DECTRIS EIGER X 9M		2023-06-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32XU	1.0	SPring-8	BL32XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	46.5	100	0.999	25.2	62.2		8896

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95			0.776

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	NONE	7XZQ	2.8	46.5	8834	880	100	0.233	0.227	0.2852	86.357

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]
0.109	0.055		0.109		-0.355

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.207
r_dihedral_angle_other_2_deg	23.576
r_dihedral_angle_3_deg	18.623
r_dihedral_angle_4_deg	17.63
r_dihedral_angle_1_deg	6.485
r_lrange_it	5.401
r_lrange_other	5.4
r_angle_refined_deg	1.25
r_angle_other_deg	1.04
r_mcangle_it	1.029
r_mcangle_other	1.019
r_scangle_it	0.895
r_scangle_other	0.895
r_mcbond_it	0.595
r_mcbond_other	0.585
r_scbond_it	0.505
r_scbond_other	0.504
r_nbd_refined	0.191
r_nbd_other	0.189
r_symmetry_nbd_other	0.174
r_nbtor_refined	0.157
r_symmetry_nbd_refined	0.153
r_xyhbond_nbd_refined	0.111
r_symmetry_xyhbond_nbd_refined	0.079
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.041
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2461
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	19

Software

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