3BQR

Crystal structure of human death associated protein kinase 3 (DAPK3) in complex with an imidazo-pyridazine ligand

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	25% 1,2-propanediol, 10% Glycerol, 0.1M Na/K phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.05	59.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.533	α = 90
b = 83.533	β = 90
c = 113.693	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	CCD	MARMOSAIC 225 mm CCD		2007-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.98248	SLS	X10SA

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	1.75	50	94.8	0.061	0.061	15.1	8.5	41297	39150

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	1.75	1.81	98.9		0.894	0.894	2.22	7.4	3999

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1YRP	1.75	35	39058	39058	1965	94.72	0.181	0.181	0.18	0.215	RANDOM	24.304

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]
0.02			0.02		-0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.379
r_dihedral_angle_4_deg	20.883
r_dihedral_angle_3_deg	13.419
r_scangle_it	9.705
r_scbond_it	7.357
r_dihedral_angle_1_deg	5.74
r_mcangle_it	4.454
r_mcbond_it	3.064
r_angle_refined_deg	1.482
r_angle_other_deg	1.421

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.379
r_dihedral_angle_4_deg	20.883
r_dihedral_angle_3_deg	13.419
r_scangle_it	9.705
r_scbond_it	7.357
r_dihedral_angle_1_deg	5.74
r_mcangle_it	4.454
r_mcbond_it	3.064
r_angle_refined_deg	1.482
r_angle_other_deg	1.421
r_mcbond_other	1.008
r_chiral_restr	0.112
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2182
Nucleic Acid Atoms
Solvent Atoms	304
Heterogen Atoms	40

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.