6QAT | pdb_00006qat

Crystal structure of ULK2 in complexed with hesperadin

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, SITTING DROP		293.15	27.5% PEG 3350, 0.1 M sodium citrate, pH 5.9, 0.15 M MgCl2, 0.1 M bis-tris, pH 5.75, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.208	α = 90
b = 77.561	β = 97.77
c = 94.941	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 EIGER X 16M		2018-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.77	48.75	99.2	0.071	0.997	10.1	5.1		27487			82

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.77	2.92	99.3		0.758	0.884	2	5.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4WNO	2.77	48.75	26116	1357	99.05	0.21993	0.21776	0.2197	0.2616	0.2618	RANDOM	108.746

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]
3.07		-1.81	0.82		-3.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.954
r_dihedral_angle_4_deg	19.171
r_dihedral_angle_3_deg	15.867
r_dihedral_angle_1_deg	7.812
r_long_range_B_refined	7.189
r_long_range_B_other	7.189
r_scangle_other	4.997
r_mcangle_it	4.761
r_mcangle_other	4.761
r_scbond_it	3.081
r_scbond_other	3.081
r_mcbond_it	2.987
r_mcbond_other	2.987
r_angle_refined_deg	1.098
r_angle_other_deg	1.033
r_chiral_restr	0.038
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8141
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	148

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing