Experiment: 1JWH

Crystal Structure of Human Protein Kinase CK2 Holoenzyme

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DAW	POLY-ALANINE BACKBONE OF CK2A FROM ZEA MAYS (PDB ENTRY 1DAW)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.3	285	initial composition of the drop: 3 ul rhCK2 stock solution [5 mg/ml enzyme in 25 mM Tris/HCl, 300 mM NaCl, 1 mM dithiothreitole, pH 8.5], 1.5 ul reservoir solution [20 % (w/v) PEG3350, 200 mM dipotassium hydrogenphosphate], 3 ul 1 mM adenylyl imidodiphosphate (AMPPNP), 3 ul 2 mM magnesium chloride, 2 ul 10 % (w/v) polyethylene glycol 400 dodecylether (Thesit), pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
3.22	61.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 175.99	α = 90
b = 175.99	β = 90
c = 93.666	γ = 120

Symmetry
Space Group	P 63

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MARRESEARCH		2000-01-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7B	0.8428	EMBL/DESY, HAMBURG	BW7B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	3.1	59.3	98.4	0.096	16.7	8.8		29935			92.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.1	3.2	90.4		42	2.6	6

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	POLY-ALANINE BACKBONE OF CK2A FROM ZEA MAYS (PDB ENTRY 1DAW)	3.1	59.3	23733	935	78.7	0.267	0.2623	0.338	0.3368	Random	90.96

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]
-32.76	26.71		-32.76		65.51

RMS Deviations
Key	Refinement Restraint Deviation
c_scangle_it	24.14
c_dihedral_angle_d	22.2
c_scbond_it	19.26
c_mcangle_it	17.4
c_mcbond_it	12.23
c_angle_deg	1.5
c_improper_angle_d	1.05
c_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8947
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	68

Software

Software
Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling