30TQ | pdb_000030tq

14-3-3sigma protein binding to TSC2-wt peptide and stabilizer 3'deAc FC-A.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4JDD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.095 M HEPES pH=7.1-7.7 0.19 M CaCl2 5% glycerol 24-29% PEG400

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.486	α = 90
b = 112.49	β = 90
c = 63.051	γ = 90

Symmetry
Space Group	C 2 2 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 EIGER X 4M		2024-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.967697	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	45.803	99.6	0.998	19.6	10.9		38924

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63			0.918	5

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.6	45.803	38103	1972	97.535	0.186	0.1845	0.1984	0.2053	0.219	RANDOM	22.676

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]
1.101			-0.695		-0.406

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.125
r_lrange_other	13.132
r_lrange_it	13.038
r_scangle_it	12.341
r_scangle_other	12.337
r_dihedral_angle_3_deg	12.332
r_scbond_it	10.007
r_scbond_other	9.994
r_dihedral_angle_1_deg	8.507
r_mcangle_it	8.01
r_mcangle_other	8.009
r_mcbond_it	6.49
r_mcbond_other	6.49
r_dihedral_angle_2_deg	1.125
r_angle_refined_deg	0.965
r_dihedral_angle_other_2_deg	0.689
r_angle_other_deg	0.407
r_nbd_refined	0.216
r_nbtor_refined	0.167
r_symmetry_nbd_other	0.156
r_metal_ion_refined	0.144
r_xyhbond_nbd_refined	0.141
r_nbd_other	0.132
r_symmetry_nbd_refined	0.13
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.067
r_chiral_restr	0.044
r_bond_refined_d	0.005
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	1915
Nucleic Acid Atoms
Solvent Atoms	231
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB-REDO	refinement
autoPROC	data reduction
Aimless	data scaling
MOLREP	phasing