7F3G | pdb_00007f3g

Crystal structure of DCLK1 kinase domain in complex with ruxolitinib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5JZJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	25% (w/v) polyethylene glycol (PEG) 3,350, 0.1 M Bis-Tris (pH 6.5), and 200 mM magne-sium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.248	α = 90
b = 80.118	β = 90.662
c = 59.338	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	CCD	BRUKER SMART 6500		2020-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	1.0000	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.09	50	95.5	0.05	0.067	0.998	8.41	2		31156

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.21	90.8		0.725	0.833	0.662		1.92

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5JZJ	2.1	47.727	31156	1568	99.283	0.213	0.2104	0.22	0.2533	0.25	62.345

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]
1.299		-5.598	-5.637		4.467

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.211
r_dihedral_angle_4_deg	16.144
r_dihedral_angle_3_deg	13.126
r_lrange_it	7.042
r_lrange_other	7.042
r_dihedral_angle_1_deg	6.387
r_mcangle_it	4.772
r_mcangle_other	4.771
r_scangle_it	4.52
r_scangle_other	4.519
r_mcbond_it	2.882
r_mcbond_other	2.881
r_scbond_it	2.808
r_scbond_other	2.806
r_angle_refined_deg	1.138
r_angle_other_deg	1.089
r_symmetry_nbd_other	0.184
r_nbd_other	0.183
r_nbd_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.168
r_nbtor_refined	0.152
r_xyhbond_nbd_refined	0.12
r_symmetry_nbd_refined	0.076
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.04
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4236
Nucleic Acid Atoms
Solvent Atoms	51
Heterogen Atoms	46

Software

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