9CD5 | pdb_00009cd5

FGFR1 Kinase Domain Soak 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		FGFR1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	25%P8K, 25% EG, 0.25M AS, 0.1MPCTP pH7.5

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 206.03	α = 90
b = 57.614	β = 107.185
c = 65.694	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	CCD	APEX II CCD		2020-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.54184

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	2.939	49.256	99.8	0.141	0.16	0.074	0.988	7.9	4.5		15930

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	2.939	3.04	98.4		0.63	0.782	0.454	0.686	1.4	2.8

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	2.939	49.256	15924	773	99.724	0.215	0.213	0.2177	0.2629	0.262	46.308

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]
-0.44		-0.914	2.168		-0.976

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	12.953
r_dihedral_angle_3_deg	12.433
r_dihedral_angle_2_deg	12.425
r_lrange_it	7.287
r_lrange_other	7.155
r_dihedral_angle_1_deg	5.65
r_scangle_it	2.609
r_scangle_other	2.265
r_mcangle_it	1.895
r_mcangle_other	1.895
r_scbond_it	1.571
r_scbond_other	1.333
r_mcbond_it	1.072
r_mcbond_other	1.072
r_angle_refined_deg	0.914
r_angle_other_deg	0.335
r_nbd_refined	0.196
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.166
r_nbd_other	0.145
r_xyhbond_nbd_refined	0.137
r_symmetry_nbd_refined	0.1
r_ncsr_local_group_1	0.087
r_symmetry_xyhbond_nbd_other	0.075
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.043
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4539
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	151

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data scaling
SAINT	data reduction
PHASER	phasing