8W2X | pdb_00008w2x

TAS-120 covalent structure with FGFR2

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	0.2 M Potassium sodium tartrate tetrahydrate 2.0 M Ammonium sulfate 0.1 M Sodium citrate 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.62	α = 90
b = 96.62	β = 90
c = 147.1	γ = 120

Symmetry
Space Group	P 31 2 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 EIGER X 9M		2021-11-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12713	APS	21-ID-D

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	2.98	48.31	100	0.27	0.277	0.061	0.997	11.6	20.2		16789

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	2.98	3.06	99.9		1.89	1.936	0.419	0.763		21.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.98	30	15951	789	99.83	0.2113	0.21	0.2129	0.237	0.2422	RANDOM	63.787

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]
-1.15	-0.58		-1.15		3.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.467
r_dihedral_angle_4_deg	16.919
r_dihedral_angle_3_deg	15.648
r_dihedral_angle_1_deg	5.63
r_angle_refined_deg	1.193
r_angle_other_deg	1.035
r_chiral_restr	0.04
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.467
r_dihedral_angle_4_deg	16.919
r_dihedral_angle_3_deg	15.648
r_dihedral_angle_1_deg	5.63
r_angle_refined_deg	1.193
r_angle_other_deg	1.035
r_chiral_restr	0.04
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4823
Nucleic Acid Atoms
Solvent Atoms	28
Heterogen Atoms	88

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

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.