7AB1 | pdb_00007ab1

Crystal structure of MerTK kinase domain in complex with Gilteritinib

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3BRB	pdbid 3BRB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	293	0.1M Tris pH 8.5, 4.3M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.302	α = 90
b = 94.12	β = 90
c = 70.734	γ = 90

Symmetry
Space Group	C 2 2 21

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		2020-01-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.976254	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.927	46.651	88.3	0.115	0.125	0.05	0.996	9.8	5.3		18953

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.927	2.051	56.3		1.116	1.269	0.594	0.808		4.4

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	pdbid 3BRB	1.93	46.651	17788	893	78.14	0.2375	0.2344	0.243	0.2979	0.2234	RANDOM	52.816

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]
0.31			-0.69		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.856
r_dihedral_angle_4_deg	17.467
r_dihedral_angle_3_deg	14.549
r_dihedral_angle_1_deg	6.305
r_angle_refined_deg	1.534
r_angle_other_deg	0.975
r_chiral_restr	0.084
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2075
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms	48

Software

Software
Software Name	Purpose
XDS	data reduction
Aimless	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction