6QAV | pdb_00006qav

Crystal structure of ULK2 in complexed with 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, SITTING DROP		293.15	37.5% PEG 3350, 0.1 M sodium citrate, pH 5.9, 0.15 M MgCl2, 0.1 M bis-tris, pH 5.5, 5% glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.648	α = 90
b = 69.05	β = 97.93
c = 107.71	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 PILATUS3 2M		2018-06-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.000	SLS	X06DA

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	2.05	57.97	100	0.078	0.998	11.7	5.3		68365			32.4

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	2.05	2.12	99.9		0.657	0.842	2.4	5.3

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	2.05	57.97	65014	3331	99.95	0.19696	0.19518	0.2052	0.23085	0.2346	RANDOM	45.569

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]
-0.73		-0.38	2.79		-1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.759
r_dihedral_angle_4_deg	20.877
r_dihedral_angle_3_deg	15.276
r_dihedral_angle_1_deg	6.883
r_long_range_B_refined	6.569
r_long_range_B_other	6.569
r_scangle_other	3.192
r_mcangle_it	3.104
r_mcangle_other	3.104
r_scbond_it	1.982
r_scbond_other	1.982
r_mcbond_it	1.851
r_mcbond_other	1.851
r_angle_refined_deg	1.267
r_angle_other_deg	0.905
r_chiral_restr	0.071
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	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	8578
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	201

Software

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