30TR | pdb_000030tr

14-3-3sigma protein binding to TSC2-weak peptide (AAA mutation)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N75

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
2.68	54.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.532	α = 90
b = 112.59	β = 90
c = 62.819	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 EIGER2 X 9M		2024-09-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

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	1.3	66.56	100	1	25.4	13.8		72105

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	1.3	1.32			0.932	4.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.3	45.728	72078	3675	99.983	0.13	0.1286	0.1296	0.148	0.15	RANDOM	15.719

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]
1.801			-0.576		-1.225

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.679
r_lrange_it	14.864
r_dihedral_angle_3_deg	13.852
r_lrange_other	13.168
r_scangle_it	9.793
r_scangle_other	9.79
r_dihedral_angle_1_deg	7.23
r_scbond_it	6.784
r_scbond_other	6.768
r_mcangle_other	6.66
r_mcangle_it	6.654
r_mcbond_it	4.603
r_mcbond_other	4.594
r_rigid_bond_restr	3.34
r_angle_refined_deg	1.464
r_angle_other_deg	0.593
r_symmetry_xyhbond_nbd_refined	0.29
r_xyhbond_nbd_refined	0.261
r_symmetry_xyhbond_nbd_other	0.25
r_nbd_refined	0.24
r_symmetry_nbd_refined	0.202
r_nbtor_refined	0.183
r_symmetry_nbd_other	0.176
r_symmetry_metal_ion_refined	0.168
r_nbd_other	0.141
r_metal_ion_refined	0.088
r_chiral_restr	0.079
r_symmetry_nbtor_other	0.067
r_bond_refined_d	0.015
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	1901
Nucleic Acid Atoms
Solvent Atoms	268
Heterogen Atoms	6

Software

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