8P5L

Kinase domain of mutant human ULK1 in complex with compound MRT67307

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WNO

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
3.6	65.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.6	α = 90
b = 152.6	β = 90
c = 206.14	γ = 120

Symmetry
Space Group	H 3 2

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		2022-11-02	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	1.836	111.255	99.5	1	20.2	18.4		79997

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	1.836	1.867			0.81	2.3

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	1.836	111.255	79997	4146	99.545	0.177	0.1756	0.2113	32.223

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]
-0.235	-0.118		-0.235		0.762

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.165
r_dihedral_angle_3_deg	15.956
r_lrange_it	9.195
r_lrange_other	9.119
r_dihedral_angle_2_deg	8.457
r_scangle_it	7.212
r_scangle_other	7.211
r_dihedral_angle_1_deg	6.069
r_mcangle_it	4.761
r_mcangle_other	4.76
r_scbond_it	4.684
r_scbond_other	4.683
r_mcbond_it	3.449
r_mcbond_other	3.449
r_angle_refined_deg	1.663
r_angle_other_deg	0.554
r_xyhbond_nbd_refined	0.244
r_nbd_refined	0.222
r_symmetry_nbd_other	0.191
r_nbd_other	0.189
r_nbtor_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.097
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.082
r_symmetry_nbd_refined	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4296
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	72

Software

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