9V4E

Crystal Structure of Gallus gallus c-Src Kinase Domain with Point mutation Y416D and Deletion of Residues N414, T417, and R419 Bound to AMP-PNP

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL45XU
Synchrotron site	SPring-8
Beamline	BL45XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-02-05
Detector	DECTRIS PILATUS 6M
Wavelength(s)	1.00
Spacegroup name	P 21 21 21
Unit cell lengths	41.457, 62.874, 105.378
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	40.416 - 1.780
Rwork	0.200
R-free	0.24130
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	AlphaFold
RMSD bond length	0.009
RMSD bond angle	1.723
Data reduction software	XDS (Jun 30, 2024)
Data scaling software	XDS (Jun 30, 2024)
Phasing software	MOLREP (11.9.02)
Refinement software	REFMAC (5.8.0430 (refmacat 0.4.88))

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	41.460	1.890
High resolution limit [Å]	1.780	1.780
Rmerge	0.084	0.731
Rmeas	0.089	0.779
Number of reflections	27180	4326
<I/σ(I)>	19.52	2.79
Completeness [%]	99.8
Redundancy	8.13	8.35
CC(1/2)	0.999	0.852

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	5.5	283	19% PEG 3350, 5% glycerol, 0.1 M Bis-Tris pH 5.5, and 0.2 M sodium acetate Cryoprotectant: 30% PEG 400, 19% PEG 3350, 5% glycerol, 0.1 M Bis-Tris pH 5.5, and 0.2 M sodium acetate