5J31 | pdb_00005j31

Crystal structure of 14-3-3zeta in complex with an alkyne cross-linked cyclic peptide derived from ExoS

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4FJ3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	1.26 M Tri-Sodium Citrate, 0.09 M HEPES pH 7.5, 10% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
4.68	73.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.94	α = 90
b = 105.58	β = 90
c = 114.51	γ = 90

Symmetry
Space Group	P 21 21 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 PILATUS 6M		2015-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	47.94	100	0.053	1	29.54	13.28		40511		-3	62.86

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	2.4	2.6	100		0.508	5.88	13.79

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	4FJ3	2.4	47.94	38425	2025	99.96	0.1659	0.1631	0.18	0.2186	0.23	RANDOM	65.535

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]
6.09			-2.03		-4.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.276
r_dihedral_angle_3_deg	19.269
r_dihedral_angle_4_deg	19.121
r_dihedral_angle_1_deg	6.742
r_angle_refined_deg	3.387
r_angle_other_deg	1.305
r_chiral_restr	0.141
r_bond_refined_d	0.019
r_bond_other_d	0.01
r_gen_planes_refined	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.276
r_dihedral_angle_3_deg	19.269
r_dihedral_angle_4_deg	19.121
r_dihedral_angle_1_deg	6.742
r_angle_refined_deg	3.387
r_angle_other_deg	1.305
r_chiral_restr	0.141
r_bond_refined_d	0.019
r_bond_other_d	0.01
r_gen_planes_refined	0.008
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3826
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	9

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.