30TP | pdb_000030tp

14-3-3sigma protein binding to TSC2-wt peptide

X-RAY DIFFRACTION

---

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	54.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.65	α = 90
b = 112.649	β = 90
c = 62.947	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		2024-06-14	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	1.6	66.64	88	1	40.5	13.6		469510

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			0.991	11.2

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	45.801	34413	1768	87.986	0.159	0.1576	0.1574	0.18	0.1808	RANDOM	19.952

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]
0.6			-0.222		-0.379

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.434
r_dihedral_angle_3_deg	13.332
r_dihedral_angle_1_deg	8.794
r_lrange_it	6.42
r_lrange_other	6.316
r_scangle_it	5.584
r_scangle_other	5.582
r_scbond_it	3.697
r_scbond_other	3.691
r_mcangle_it	3.35
r_mcangle_other	3.35
r_mcbond_it	2.261
r_mcbond_other	2.261
r_angle_refined_deg	1.262
r_angle_other_deg	0.512
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.203
r_nbtor_refined	0.178
r_symmetry_xyhbond_nbd_refined	0.178
r_symmetry_nbd_other	0.162
r_xyhbond_nbd_refined	0.145
r_nbd_other	0.144
r_metal_ion_refined	0.132
r_symmetry_metal_ion_refined	0.091
r_symmetry_nbtor_other	0.064
r_chiral_restr	0.063
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1909
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	10

Software

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