7L1X | pdb_00007l1x

Structure of human CK2 alpha kinase (catalytic subunit) with the inhibitor 108600.

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	100 mM Tris-HCl pH 7.5 200 mM ammonium sulfate 21% PEG5000

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.348	α = 90
b = 45.981	β = 111.84
c = 63.683	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MAR CCD 165 mm		2011-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.98011	APS	23-ID-D

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	1.8	25	97.3	0.091	18.51	3.9		28233

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	1.8	1.84			0.5

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	3OWJ	1.8	24.88	26802	1418	96.92	0.1754	0.1728	0.18	0.2212	0.23	RANDOM	34.827

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]
-1.72		-0.35	1.27		0.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.281
r_dihedral_angle_4_deg	21.235
r_dihedral_angle_3_deg	13.547
r_dihedral_angle_1_deg	6.248
r_angle_refined_deg	1.225
r_angle_other_deg	0.435
r_chiral_restr	0.065
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.281
r_dihedral_angle_4_deg	21.235
r_dihedral_angle_3_deg	13.547
r_dihedral_angle_1_deg	6.248
r_angle_refined_deg	1.225
r_angle_other_deg	0.435
r_chiral_restr	0.065
r_gen_planes_refined	0.006
r_bond_refined_d	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2746
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	71

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	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.