3H30 | pdb_00003h30

Crystal structure of the catalytic subunit of human protein kinase CK2 with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	1.5M ammonium sulfate, 0.2M tri-sodium citrate, 0.2M K/Na tartrate pH 5.6, the enzyme was preincubated with 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.506	α = 90
b = 71.506	β = 90
c = 125.789	γ = 90

Symmetry
Space Group	P 43

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	MARMOSAIC 225 mm CCD		2006-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X12	0.9	EMBL/DESY, HAMBURG	X12

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.56	25	99.9			89590	89486

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	SAD	THROUGHOUT	1.56	25	89590	87584	1860	99.91	0.15666	0.15666	0.15578	0.2	0.19811	0.23	RANDOM	23.844

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]
-1.02			-1.02		2.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.235
r_dihedral_angle_3_deg	13.674
r_dihedral_angle_4_deg	13.665
r_dihedral_angle_1_deg	5.708
r_scangle_it	4.01
r_scbond_it	3.211
r_mcangle_it	2.495
r_mcbond_it	1.948
r_angle_refined_deg	1.189
r_mcbond_other	0.92
r_angle_other_deg	0.84
r_chiral_restr	0.072
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5667
Nucleic Acid Atoms
Solvent Atoms	617
Heterogen Atoms	92

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling