6NCG

Crystal Structure of Human Vaccinia-related kinase 2 (VRK-2) bound to pyridin-benzenesulfonamide inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5UU1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	293	27.5% PEG3350; 200 mM LiSO4; 0.1M SBG (each Sodium-tartrate + Bis-Tris + Glycylglycine) pH 6.0

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.528	α = 90
b = 67.625	β = 90
c = 171.346	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	CCD	ADSC QUANTUM 315r		2017-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.979100	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.45	29.1	99.9	0.137	0.15	0.061	0.998	10.8	10.6		24095

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.45	2.55	99.9		1.773	1.96	0.824	0.707	1.2	10.3

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5UU1	2.45	29.1	22794	1241	99.75	0.22443	0.22061	0.29694	RANDOM	65.063

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]
-4.63			11.7		-7.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.996
r_dihedral_angle_3_deg	14.575
r_dihedral_angle_4_deg	13.401
r_long_range_B_refined	11.299
r_long_range_B_other	11.298
r_mcangle_it	6.337
r_mcangle_other	6.336
r_scangle_other	6.086
r_dihedral_angle_1_deg	5.043
r_mcbond_it	3.925
r_mcbond_other	3.925
r_scbond_it	3.8
r_scbond_other	3.8
r_angle_refined_deg	1.199
r_angle_other_deg	0.779
r_chiral_restr	0.062
r_bond_refined_d	0.008
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	4466
Nucleic Acid Atoms
Solvent Atoms	41
Heterogen Atoms	57

Software

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