6YUL | pdb_00006yul

CK2 alpha bound to Macrocycle

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PE2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.2 M ammonia sulphate, 0.1 MES pH 6.5, 31-35% (v/v) polyethylene glycol PEG 5000 MME 10 mg / mL protein

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.649	α = 90
b = 128.649	β = 90
c = 125.454	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		2018-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.999998	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	2.4	45.48	100	0.027	0.999	16.9	14.9		41786

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	2.4	2.49			0.426	0.718

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	3PE2	2.4	45.48	41726	2065	99.976	0.218	0.2168	0.22	0.2324	0.23	56.533

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]
0.21			0.21		-0.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.73
r_dihedral_angle_4_deg	16.248
r_dihedral_angle_3_deg	14.888
r_lrange_it	8.078
r_lrange_other	8.078
r_dihedral_angle_1_deg	6.428
r_scangle_it	5.282
r_scangle_other	5.26
r_mcangle_it	4.993
r_mcangle_other	4.993
r_scbond_it	3.297
r_scbond_other	3.275
r_mcbond_it	3.108
r_mcbond_other	3.107
r_angle_other_deg	1.512
r_angle_refined_deg	1.459
r_nbd_refined	0.219
r_nbtor_refined	0.178
r_symmetry_nbd_other	0.174
r_symmetry_nbd_refined	0.165
r_nbd_other	0.165
r_symmetry_xyhbond_nbd_refined	0.158
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.08
r_ext_dist_refined_d	0.048
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_symmetry_xyhbond_nbd_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5450
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	100

Software

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