9CD7 | pdb_00009cd7

FGFR3 Kinase Domain with Inhibitor TYRA-300

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		FGFR3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.25	291	17% PEG Smear Medium 10% Tacsimate pH 5.25 0.2M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.686	α = 90
b = 55.588	β = 127.452
c = 138.668	γ = 90

Symmetry
Space Group	C 1 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 PILATUS3 2M		2024-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1	ALS	8.2.2

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	2.53	48.17	99.8	0.443	0.48	0.183	0.966	4.7	6.8		36870

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	2.53	2.64		100	3.534	3.817	1.428	0.21		7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.53	40.003	36861	1654	99.765	0.23	0.2287	0.2326	0.2671	0.2694	54.443

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]
-0.865		-1.008	1.966		0.203

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.024
r_dihedral_angle_6_deg	11.556
r_dihedral_angle_2_deg	11.196
r_lrange_other	9.418
r_lrange_it	9.416
r_scangle_it	6.789
r_scangle_other	6.59
r_dihedral_angle_1_deg	6.16
r_mcangle_other	6.064
r_mcangle_it	6.062
r_scbond_it	4.321
r_scbond_other	4.085
r_mcbond_it	3.813
r_mcbond_other	3.803
r_angle_refined_deg	1.037
r_angle_other_deg	0.381
r_symmetry_xyhbond_nbd_refined	0.301
r_symmetry_nbd_refined	0.205
r_nbd_refined	0.2
r_nbd_other	0.19
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.143
r_ncsr_local_group_2	0.083
r_ncsr_local_group_3	0.077
r_symmetry_nbtor_other	0.074
r_ncsr_local_group_1	0.073
r_chiral_restr	0.052
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6577
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	227

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing