9SAE | pdb_00009sae

14-3-3sigma protein binding to ChREBP peptide and macrocycle 4

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YGJ

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
2.59	52.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.866	α = 90
b = 112.997	β = 90
c = 63.468	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 9M		2024-04-10	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	2.3	56.56	92.72	0.98	5.5	7.6		128946

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	2.3	2.53			0.502	1.8

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 (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	2.3	56.56	12003	606	92.75	0.2299	0.22712	0.2358	0.2848	0.2914	RANDOM	35.951

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]
1.77			-1.06		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.513
r_dihedral_angle_3_deg	13.055
r_long_range_B_refined	9.295
r_long_range_B_other	9.291
r_scangle_other	6.939
r_dihedral_angle_1_deg	5.9
r_mcangle_it	5.08
r_mcangle_other	5.079
r_scbond_it	4.349
r_scbond_other	4.347
r_mcbond_it	3.48
r_mcbond_other	3.461
r_angle_refined_deg	0.783
r_angle_other_deg	0.335
r_chiral_restr	0.035
r_bond_refined_d	0.005
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1935
Nucleic Acid Atoms
Solvent Atoms	68
Heterogen Atoms	63

Software

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