7VJL | pdb_00007vjl

The crystal structure of FGFR4 kinase domain in complex with N-(5-cyano-4-((2-methoxyethyl)amino)pyridin-2-yl)-7-(2,2,2-trifluoroacetyl)-3,4-dihydro-1,8-naphthyridine-1(2H)-carboxamide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6JPJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.5m NH4H2PO4

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.37	α = 90
b = 66.785	β = 90
c = 184.174	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS 300K		2020-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CAMD BEAMLINE GCPCC	0.978690	CAMD	GCPCC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.9	50	99.5	0.915	10.14	4.4		15232			47.6659209837

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3			0.779

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6JPJ	2.90017299719	37.9076086709	1.37094337122	15083	1509	98.8530606895	0.211575321392	0.204653382216	0.21	0.273007589253	0.27	51.90497332

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	12.1869576763
f_angle_d	0.785204165568
f_chiral_restr	0.0721141260256
f_plane_restr	0.00333753016453
f_bond_d	0.00299665953234

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4122
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	64

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
Coot	model building
PHASER	phasing
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.