5TS8 | pdb_00005ts8

Z. MAYS CK2 KINASE ALPHA SUBUNIT IN COMPLEX WITH THE ATP-COMPETITIVE INHIBITOR 5,6-DIBROMOBENZOTRIAZOLE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RLK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	pH 7.5 (1M Sodium HEPES; MOPS), 40% v/v PEG 500* MME; 20 % w/v PEG 20K; 0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.311	α = 90
b = 59.726	β = 90
c = 105.385	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2015-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9116	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	CC (Half)	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	1.45	51.96	98	0.057	0.048	0.99	14.19	3.23		60461			22.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.54	95.9		0.55	0.84	2.81	2.78

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	4RLK	1.45	51.96	57482	2923	98	0.14989	0.14888	0.16	0.16945	0.18	RANDOM	22.744

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]
-0.76			-0.9		1.66

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.199
r_dihedral_angle_4_deg	18.418
r_dihedral_angle_3_deg	13.206
r_long_range_B_refined	5.964
r_long_range_B_other	5.489
r_dihedral_angle_1_deg	5.425
r_scangle_other	2.589
r_mcangle_it	2.209
r_mcangle_other	2.208
r_scbond_it	1.532
r_scbond_other	1.531
r_angle_refined_deg	1.454
r_mcbond_it	1.317
r_mcbond_other	1.317
r_angle_other_deg	0.972
r_chiral_restr	0.103
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_gen_planes_other	0.004
r_bond_other_d	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2774
Nucleic Acid Atoms
Solvent Atoms	453
Heterogen Atoms	60

Software

Software
Software Name	Purpose
XDS	data reduction
XDS	data scaling
MOLREP	phasing
WARP	model building
REFMAC	refinement
ARP/wARP	phasing