8P5G | pdb_00008p5g

Kinase domain of wild type 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
3.62	65.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.8	α = 90
b = 111.67	β = 90
c = 84.5	γ = 90

Symmetry
Space Group	P 21 21 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		2022-05-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.9999	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	2.019	67.383	100	0.999	16.9	11.6		60175

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	2.019	2.054	100		0.789	2.2	11.4

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	2.019	67.383	60175	3109	99.927	0.186	0.1839	0.19	0.2269	0.23	45.019

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]
2.644			-1.843		-0.801

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.078
r_dihedral_angle_3_deg	15.453
r_lrange_other	9.235
r_lrange_it	9.232
r_dihedral_angle_2_deg	8.614
r_scangle_it	7.908
r_scangle_other	7.907
r_dihedral_angle_1_deg	6.03
r_scbond_it	5.43
r_scbond_other	5.429
r_mcangle_it	4.98
r_mcangle_other	4.979
r_mcbond_it	3.96
r_mcbond_other	3.948
r_angle_refined_deg	1.47
r_angle_other_deg	0.498
r_nbd_other	0.22
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.198
r_nbtor_refined	0.188
r_symmetry_nbd_refined	0.15
r_symmetry_xyhbond_nbd_refined	0.144
r_ncsr_local_group_1	0.102
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.023
r_chiral_restr_other	0.019
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4284
Nucleic Acid Atoms
Solvent Atoms	291
Heterogen Atoms	70

Software

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