8P5K | pdb_00008p5k

Kinase domain of mutant human ULK1 in complex with compound MRT68921

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
3.5	64.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.26	α = 90
b = 109.94	β = 93.775
c = 96.22	γ = 90

Symmetry
Space Group	P 1 21 1

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		2023-05-05	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	2.209	85.075	99.7	0.999	16.6	6.6		88463

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	2.209	2.247	99.2		0.714	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.209	85.075	88461	4466	99.649	0.178	0.177	0.18	0.2043	0.21	40.344

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]
0.246		-1.165	-1.31		1.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.703
r_dihedral_angle_6_deg	16.695
r_dihedral_angle_2_deg	10.849
r_dihedral_angle_other_2_deg	10.202
r_lrange_it	9.143
r_lrange_other	9.136
r_scangle_it	7.675
r_scangle_other	7.671
r_dihedral_angle_1_deg	6.167
r_mcangle_it	5.104
r_mcangle_other	5.103
r_scbond_it	4.977
r_scbond_other	4.957
r_mcbond_it	3.605
r_mcbond_other	3.604
r_angle_refined_deg	1.427
r_angle_other_deg	0.478
r_nbd_refined	0.221
r_xyhbond_nbd_refined	0.208
r_symmetry_nbd_other	0.2
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.182
r_nbd_other	0.18
r_symmetry_xyhbond_nbd_refined	0.123
r_ncsr_local_group_6	0.1
r_ncsr_local_group_3	0.098
r_ncsr_local_group_4	0.096
r_ncsr_local_group_1	0.093
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_2	0.08
r_ncsr_local_group_5	0.075
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.027
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	8649
Nucleic Acid Atoms
Solvent Atoms	617
Heterogen Atoms	164

Software

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