9V4E | pdb_00009v4e

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
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

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.457	α = 90
b = 62.874	β = 90
c = 105.378	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 6M		2024-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.78	41.46	99.8	0.084	0.089	0.999	19.52	8.13		27180

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.78	1.89			0.731	0.779	0.852	2.79	8.35

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	AlphaFold	1.78	40.416	27180	1348	99.776	0.202	0.2001	0.21	0.2413	0.249	32.111

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]
0.159			-0.132		-0.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.504
r_dihedral_angle_3_deg	11.596
r_dihedral_angle_2_deg	8.05
r_lrange_it	7.749
r_lrange_other	7.738
r_dihedral_angle_1_deg	6.749
r_scangle_it	5.937
r_scangle_other	5.935
r_mcangle_it	4.455
r_mcangle_other	4.454
r_scbond_it	3.997
r_scbond_other	3.997
r_mcbond_it	3.23
r_mcbond_other	3.23
r_angle_refined_deg	1.723
r_angle_other_deg	0.574
r_symmetry_nbd_refined	0.32
r_nbd_refined	0.224
r_nbtor_refined	0.188
r_nbd_other	0.188
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.13
r_chiral_restr_other	0.086
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.084
r_metal_ion_refined	0.056
r_dihedral_angle_other_2_deg	0.024
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1925
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	32

Software

Software
Software Name	Purpose
XDS	data scaling
XDS	data reduction
MOLREP	phasing
REFMAC	refinement