6FNC | pdb_00006fnc

Mono- and bivalent 14-3-3 inhibitors for characterizing supramolecular lysine-PEG interactions in proteins

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NKX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277.15	0.18 M Magnesium chloride, 0.09 M Sodium HEPES pH 7.5 10%(v/v) Glycerol 27%(v/v) Isopropanol

Crystal Properties
Matthews coefficient	Solvent content
4.01	69.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.999	α = 90
b = 102.992	β = 90
c = 113.875	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		2016-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.978540	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.12	44.66	99.3	0.104	0.108	0.997	13.94	13.236		48590			57.308

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.12	2.25	95.8		1.394	1.45	0.696	1.57	12.963

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	3NKX	2.12	44.66	46098	2426	99.31	0.2177	0.2162	0.22	0.2463	0.25	RANDOM	55.208

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]
-0.06			2.68		-2.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.688
r_dihedral_angle_4_deg	16.131
r_dihedral_angle_3_deg	13.567
r_dihedral_angle_1_deg	5.084
r_angle_refined_deg	1.084
r_angle_other_deg	1.013
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_bond_other_d	0.003
r_gen_planes_refined	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.688
r_dihedral_angle_4_deg	16.131
r_dihedral_angle_3_deg	13.567
r_dihedral_angle_1_deg	5.084
r_angle_refined_deg	1.084
r_angle_other_deg	1.013
r_chiral_restr	0.052
r_bond_refined_d	0.007
r_bond_other_d	0.003
r_gen_planes_refined	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3562
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms	112

Software

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

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.