8P5H

Kinase domain of mutant human ULK1 in complex with compound CCT241533

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
3.46	64.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.65	α = 90
b = 96.31	β = 90
c = 109.19	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		2022-11-02	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	1.941	66.9	100	0.999	16.9	12.6		66660

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	1.941	1.974	100		0.682	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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.941	66.9	66658	3377	99.97	0.171	0.1698	0.193	35.553

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]
-0.564			0.148		0.417

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.624
r_dihedral_angle_3_deg	15.557
r_lrange_it	8.914
r_lrange_other	8.874
r_scangle_it	7.73
r_scangle_other	7.729
r_dihedral_angle_2_deg	7.628
r_dihedral_angle_1_deg	5.907
r_scbond_it	5.138
r_scbond_other	5.137
r_mcangle_other	4.472
r_mcangle_it	4.471
r_mcbond_other	3.534
r_mcbond_it	3.533
r_angle_refined_deg	1.596
r_angle_other_deg	0.527
r_nbd_refined	0.224
r_xyhbond_nbd_refined	0.218
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.185
r_nbd_other	0.163
r_symmetry_xyhbond_nbd_refined	0.124
r_ncsr_local_group_1	0.088
r_chiral_restr	0.083
r_symmetry_nbd_refined	0.083
r_symmetry_nbtor_other	0.081
r_chiral_restr_other	0.02
r_symmetry_xyhbond_nbd_other	0.017
r_bond_refined_d	0.01
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	348
Heterogen Atoms	70

Software

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