8VCF | pdb_00008vcf

Crystal structure of Superbinder Src SH2 domain with Cysteine to Serine mutations

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F59	Triple mutant Src SH2 domain bound to phosphotyrosine

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	VAPOR DIFFUSION,SITTING DROP, TEMPERATURE 290K 0.2 M Ammonium Fluoride, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.481	α = 90
b = 67.481	β = 90
c = 46.886	γ = 120

Symmetry
Space Group	P 61

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	ADSC QUANTUM 210r	SI 111 CRYSTAL	2023-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9794	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.5	46.89	100	0.074	22.5	12.3		19583

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.53	99.8		0.65	3.8	11.4

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 (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	PDB ENTRY 4F59	1.5	33.74	18935	601	99.88	0.13853	0.13733	0.1437	0.17664	0.1798	RANDOM	33.101

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]
0.47	0.23		0.47		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.672
r_rigid_bond_restr	20.896
r_dihedral_angle_3_deg	14.743
r_dihedral_angle_4_deg	14.314
r_scbond_it	9.187
r_scbond_other	9.182
r_scangle_other	8.807
r_mcbond_it	7.88
r_mcbond_other	7.856
r_long_range_B_refined	7.766
r_long_range_B_other	7.587
r_dihedral_angle_1_deg	7.456
r_mcangle_it	7.317
r_mcangle_other	7.311
r_angle_refined_deg	1.856
r_angle_other_deg	1.497
r_chiral_restr	0.088
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	852
Nucleic Acid Atoms
Solvent Atoms	120
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-3000	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement