1LPU | pdb_00001lpu

Low Temperature Crystal Structure of the Apo-form of the catalytic subunit of protein kinase CK2 from Zea mays

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A6O	PDB entry 1a6o

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.1	293	PEG3350, Tris/HCl, sodium acetate, pH 8.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.19	α = 90
b = 59.758	β = 103.41
c = 45.082	γ = 90

Symmetry
Space Group	C 1 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	IMAGE PLATE	MACSCIENCE	double mirrors	1998-08-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR571	1.5418

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	1.86	69.6	99	0.084	28.4	8.8	31554	31230			18

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)
	1.86	1.92	89.8		0.473	4	7.5	2845

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1a6o	1.86	69.01	29657	1572	99.56	0.20637	0.20421	0.22	0.2476	0.26	RANDOM	22.307

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]
-1.77		-1.45	1.25		-0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.592
r_dihedral_angle_1_deg	4.019
r_scangle_it	3.408
r_scbond_it	2.14
r_mcangle_it	1.512
r_angle_refined_deg	1.438
r_angle_other_deg	1.264
r_mcbond_it	0.86
r_symmetry_vdw_other	0.277
r_nbd_refined	0.24
r_symmetry_hbond_refined	0.222
r_nbd_other	0.219
r_xyhbond_nbd_refined	0.206
r_symmetry_vdw_refined	0.152
r_xyhbond_nbd_other	0.124
r_chiral_restr	0.096
r_bond_refined_d	0.016
r_gen_planes_other	0.01
r_gen_planes_refined	0.007
r_symmetry_hbond_other	0.002
r_bond_other_d
r_nbtor_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2744
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	9

Software

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