6Z84 | pdb_00006z84

CK2 alpha bound to chemical probe SGC-CK2-1 derivative

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YUL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M bis-tris pH 5.5 23-26% (v/v) PEG 3350 0.2 M ammonia sulphate

Crystal Properties
Matthews coefficient	Solvent content
3.08	60.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.352	α = 90
b = 126.352	β = 90
c = 124.514	γ = 90

Symmetry
Space Group	P 43 21 2

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 2M-F		2020-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.99999	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	2.5	44.67	100	0.056	0.998	12.7	13.2		35531

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.6			0.415	0.845	2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6yul	2.5	44.67	35475	1850	99.969	0.217	0.215	0.22	0.2501	0.25	39.771

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]
2.362			2.362		-4.723

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.021
r_dihedral_angle_4_deg	18.479
r_dihedral_angle_3_deg	15.502
r_dihedral_angle_1_deg	6.248
r_lrange_it	4.587
r_lrange_other	4.525
r_mcangle_it	2.667
r_mcangle_other	2.667
r_scangle_other	2.563
r_scangle_it	2.56
r_mcbond_it	1.556
r_mcbond_other	1.556
r_angle_other_deg	1.49
r_scbond_it	1.482
r_scbond_other	1.482
r_angle_refined_deg	1.406
r_nbd_refined	0.218
r_nbd_other	0.211
r_symmetry_nbd_refined	0.187
r_symmetry_nbd_other	0.181
r_nbtor_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.124
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.08
r_ext_dist_refined_d	0.051
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5415
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	116

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing