8P5J

Kinase domain of mutant human ULK1 in complex with compound WZ4003

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277.15	0.3-0.8 M NaAcetate pH 6, 20-26% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
3.42	64.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.09	α = 90
b = 96.09	β = 90
c = 108.9	γ = 90

Symmetry
Space Group	P 2 21 21

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		2022-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

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	2.164	63.281	99.9	0.999	19.4	12.6		47753

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	2.164	2.201	100		0.697	2.1

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	2.164	63.281	47753	2331	99.937	0.169	0.1676	0.2001	46.156

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]
0.393			-0.029		-0.364

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.799
r_dihedral_angle_3_deg	15.83
r_dihedral_angle_2_deg	11.021
r_lrange_it	9.763
r_lrange_other	9.76
r_scangle_it	8.439
r_scangle_other	8.438
r_dihedral_angle_1_deg	6.267
r_scbond_it	5.668
r_scbond_other	5.668
r_mcangle_it	5.295
r_mcangle_other	5.294
r_mcbond_it	3.997
r_mcbond_other	3.987
r_angle_refined_deg	1.525
r_angle_other_deg	0.502
r_nbd_refined	0.221
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.186
r_nbd_other	0.186
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.12
r_ncsr_local_group_1	0.096
r_symmetry_xyhbond_nbd_refined	0.088
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.077
r_symmetry_xyhbond_nbd_other	0.053
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4297
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
MOLREP	phasing