3K2L | pdb_00003k2l

Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VX3	PDB ENTRY 2VX3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	1.26M (NH4)2SO4, 0.20M Li2SO4, 0.1M TRIS pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.285	α = 90
b = 84.285	β = 90
c = 148.505	γ = 90

Symmetry
Space Group	P 42 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	CCD	ADSC QUANTUM 315r		2009-06-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.36	42.19	99.8	0.082	0.082	12.2	6.2	22847	22801			63.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.36	2.49	100		0.899	0.899	2.1	6.4	3275

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 2VX3	2.36	40.54	22758	22694	1160	99.72	0.228	0.228	0.225	0.22	0.288	0.28	RANDOM	35.014

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]
1.53			1.53		-3.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.874
r_dihedral_angle_4_deg	20.908
r_dihedral_angle_3_deg	16.034
r_scangle_it	12.453
r_scbond_it	10.724
r_dihedral_angle_1_deg	6.918
r_mcangle_it	6.116
r_mcbond_it	4.196
r_angle_refined_deg	1.602
r_mcbond_other	1.248

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.874
r_dihedral_angle_4_deg	20.908
r_dihedral_angle_3_deg	16.034
r_scangle_it	12.453
r_scbond_it	10.724
r_dihedral_angle_1_deg	6.918
r_mcangle_it	6.116
r_mcbond_it	4.196
r_angle_refined_deg	1.602
r_mcbond_other	1.248
r_angle_other_deg	0.915
r_chiral_restr	0.092
r_bond_refined_d	0.014
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	3143
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	13

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.