6PJX | pdb_00006pjx

Crystal Structure of G Protein-Coupled Receptor Kinase 5 (GRK5) in Complex with Calmodulin (CaM)

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	Sample- 25 mg/ml GRK5/CaM complex in buffer 20 mM Hepes, pH 7.2, 200 mM NaCl, 2 mM CaCl2, 1 mM DTT incubated with SGV in the presence of MgCl2. Crystallization screening reservoir condition- 90% of (200 mM KCl, 50 mM Hepes pH 7.5, 30% 5/4 PO/OH) + 10% of (0.05% w/v L-Citrulline, 0.05% w/v Glycine, 0.05% w/v L-(-)-Threonine, 0.05% w/v L-(+)-Lysine, 0.05% w/v L-Alanine, 0.05% w/v L-Arginine, 0.05% w/v L-Asparagine monohydrate, 0.05% w/v L-Aspartic acid, 0.05% w/v L-Glutamic acid, 0.05% w/v L-Glutamine, 0.05% w/v L-Histidine, 0.05% w/v L-Isoleucine, 0.05% w/v L-Leucine, 0.05% w/v L-Methionine, 0.05% w/v L-Phenylalanine, 0.05% w/v L-Proline, 0.05% w/v L-Serine, 0.05% w/v L-Tryptophan, 0.05% w/v L-Tyrosine, 0.05% w/v L-Valine, 0.02 M HEPES sodium pH 6)

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.875	α = 90
b = 83.061	β = 90
c = 137.521	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	93.15	PIXEL	DECTRIS PILATUS 200K	Varimax-HF Confocal Optical system	2015-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.958	49.01	88.5	0.1077	14.03	3.9		51717			23.97

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	1.96	2.03	63.7		0.5964	2	2.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4TNB	1.96	49.01	1.34	93159	3591	83.7	0.197	0.196	0.2	0.23	0.23	Random	35.47

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	5.47
f_angle_d	0.901
f_chiral_restr	0.054
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4933
Nucleic Acid Atoms
Solvent Atoms	520
Heterogen Atoms	24

Software

Software
Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

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.