6FDZ | pdb_00006fdz

Unc-51-Like Kinase 3 (ULK3) In Complex With Momelotinib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WNP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1 M HEPES pH 7.5, 0.2 M MgCl2, 30% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.836	α = 90
b = 75.836	β = 90
c = 214.691	γ = 120

Symmetry
Space Group	P 61 2 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		2017-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.55	214.69	100	0.14	17	18.7		12814

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59	100		1.636	2.2	19.7

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	4wnp	2.55	65.68	12141	606	99.99	0.23379	0.23043	0.23	0.30109	0.31	RANDOM	58.642

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]
1.41	0.7		1.41		-4.57

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.124
r_dihedral_angle_4_deg	21.994
r_dihedral_angle_3_deg	15.654
r_long_range_B_refined	9.179
r_long_range_B_other	9.177
r_dihedral_angle_1_deg	7.255
r_scangle_other	6.952
r_mcangle_other	6.927
r_mcangle_it	6.926
r_mcbond_it	4.847
r_mcbond_other	4.845
r_scbond_it	4.818
r_scbond_other	4.816
r_angle_refined_deg	1.683
r_angle_other_deg	1.01
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	2029
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing