3KVW | pdb_00003kvw

Crystal Structure of dual-specificity tyrosine phosphorylation regulated kinase 2 (DYRK2) in complex with an indirubin ligand

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3K2L	PDB ENTRY 3K2L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	0.2M Na(Acetate), 0.1M cacodylate pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.28	α = 90
b = 84.28	β = 90
c = 149.12	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		2009-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9802	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	2.28	46.552	100	0.105	0.105	12.2	7.4	25294	25294			48.8

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	2.28	2.4	100		0.885	0.885	2.5	7.6	3617

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 3K2L	2.28	42.81	25362	25247	1292	99.94	0.211	0.211	0.209	0.21	0.26	0.26	RANDOM	22.469

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]
0.34			0.34		-0.69

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.292
r_dihedral_angle_4_deg	21.525
r_dihedral_angle_3_deg	16.523
r_scangle_it	10.267
r_dihedral_angle_1_deg	8.519
r_scbond_it	8.396
r_mcangle_it	5.217
r_mcbond_it	3.633
r_angle_refined_deg	1.548
r_mcbond_other	1.146

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.292
r_dihedral_angle_4_deg	21.525
r_dihedral_angle_3_deg	16.523
r_scangle_it	10.267
r_dihedral_angle_1_deg	8.519
r_scbond_it	8.396
r_mcangle_it	5.217
r_mcbond_it	3.633
r_angle_refined_deg	1.548
r_mcbond_other	1.146
r_angle_other_deg	0.939
r_chiral_restr	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3188
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	29

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
GDA	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.