6GZM | pdb_00006gzm

Crystal Structure of Human CKIdelta with A86

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293.15	The construct used for crystallization was that of the wild type protein with the mutation R13N. Crystals of CK1d in complex with A-86 were obtained using hanging drop vapour diffusion set-ups. CK1d at a concentration of 13.6 mg/ml (50 mM HEPES, 266 mM NaCl, 1 mM EDTA, 1 mM DTT, 5 mM B-OG, pH 7.5) was pre-incubated with 2 mM (5.1-fold molar excess) of A-86 (150 mM in DMSO) for 1 h. 1 ul of the protein solution was then mixed with 1 ul of reservoir solution (0.1 M Na3-Citrate, pH 4.9, 18 %(w/v) PEG 3350) and equilibrated at 20 C over 0.4 ml of reservoir solution. Well diffracting crystals appeared over night

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.232	α = 90
b = 73.659	β = 103.57
c = 89.204	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	110.15	PIXEL	DECTRIS PILATUS3 2M		2016-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.966	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.59	29.19	96.5	0.09	7.1	2.4		80180

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.59	1.68	96.4		0.57		2.4

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	3uyt	1.59	29.19	75238	3911	95.1	0.19153	0.18869	0.2	0.24976	0.26	RANDOM	28.076

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]
-0.44		-0.39	2.91		-2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.786
r_dihedral_angle_3_deg	14.524
r_dihedral_angle_4_deg	12.634
r_long_range_B_refined	10.403
r_long_range_B_other	9.764
r_dihedral_angle_1_deg	6.179
r_scangle_other	5.251
r_mcangle_it	3.838
r_mcangle_other	3.837
r_scbond_it	3.513
r_scbond_other	3.512
r_mcbond_it	2.767
r_mcbond_other	2.767
r_angle_refined_deg	1.533
r_angle_other_deg	0.985
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	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	4788
Nucleic Acid Atoms
Solvent Atoms	832
Heterogen Atoms	87

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling