1LR4 | pdb_00001lr4

Room 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	1HCL	BACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	PEG4000, sodium acetate, Tris/HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 142.55	α = 90
b = 61.44	β = 103.06
c = 45.41	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	277	IMAGE PLATE	MARRESEARCH	Mirrors	1996-10-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.1	MPG/DESY, HAMBURG	BW6

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	2	26.2	94	0.106		2.8	25896	24342			15.2

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)
	2	2.11	84.9		0.111		1.7

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	BACKBONE OF CYCLIN-DEPENDENT KINASE 2 (PDB entry 1HCL)	2	26	23092	1247	93.68	0.19487	0.19254	0.2	0.23675	0.24	RANDOM	27.212

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]
-2.27		-1.32	2.2		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	15.714
r_dihedral_angle_1_deg	4.069
r_scangle_it	3.805
r_scbond_it	2.34
r_mcangle_it	1.649
r_angle_refined_deg	1.52
r_angle_other_deg	1.287
r_mcbond_it	0.926
r_symmetry_hbond_refined	0.465
r_nbd_refined	0.248
r_symmetry_vdw_other	0.226
r_nbd_other	0.224
r_xyhbond_nbd_refined	0.215
r_symmetry_vdw_refined	0.198
r_xyhbond_nbd_other	0.145
r_symmetry_hbond_other	0.142
r_chiral_restr	0.099
r_bond_refined_d	0.016
r_gen_planes_other	0.013
r_gen_planes_refined	0.008
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	2769
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	9

Software

Software
Software Name	Purpose
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	model building
REFMAC	refinement
CCP4	data scaling
X-PLOR	phasing