7SHQ | pdb_00007shq

Structure of a functional construct of eukaryotic elongation factor 2 kinase in complex with calmodulin.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PDT	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV
experimental model	PDB	3LKM	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV
experimental model	PDB	4KUJ	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV
experimental model	PDB	1IA9	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV
experimental model	PDB	6NX4	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV
experimental model	PDB	4OZS	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV
experimental model	PDB	3RJV	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6.9	298.15	Cocktail solution: Peg3350: 24% MgCl2: 300 mM BisTris pH 6.9: 100 mM Protein Solution: 11 mg/mL CaM-eEF2Kp1/1 Tris pH 7.5: 20 mM NaCl: 0.1 M CaCl2: 3mM TCEP: 1mM MgCl2: 1.5 mM AMPPNP: 1.0 mM Crystallization conditions: 1/1 Protein/Cocktail under Paraffin Oil in a Greiner 72-Well microbatch plate

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.495	α = 90
b = 58.495	β = 90
c = 365.779	γ = 120

Symmetry
Space Group	P 31 2 1

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		2021-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.97946	NSLS-II	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.34	121.9	100	0.362	0.137	0.073	0.994	14.5	25.9		32010			14.98

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.342	2.382	100		1.778	1.817	0.368	0.943	2.5	24.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3PDT,3LKM,4KUJ,1IA9,6NX4,4OZS,3RJV	2.34	50.66	1.34	31982	1514	99.9	0.2304	0.2293	0.23	0.252	0.25	33.65

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	6.504
f_angle_d	0.6114
f_chiral_restr	0.0412
f_plane_restr	0.0039
f_bond_d	0.0034

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5106
Nucleic Acid Atoms
Solvent Atoms	143
Heterogen Atoms	8

Software

Software
Software Name	Purpose
PHENIX	refinement
ISOLDE	refinement
Coot	model building
MR-Rosetta	phasing
autoPROC	data scaling
autoPROC	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.