4PF4

1.1A X-RAY STRUCTURE OF THE APO CATALYTIC DOMAIN OF DEATH-ASSOCIATED PROTEIN KINASE 1, aa 1-277

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2W4J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	292	0.1 M HEPES, Ph=7, 2M Ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.516	α = 90
b = 62.005	β = 90
c = 88.375	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	PIXEL	DECTRIS PILATUS 6M-F		2014-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.973	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.129	50.758	99.4	0.076	0.082	0.032	10.7	6.3	96009	96009

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.13	1.19	96.5		0.709	0.709	0.341	1.1	5	13431

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	2W4J	1.13	50.758	95914	4805	99.36	0.1183	0.1167	0.1495	RANDOM	16.198

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]
-1.09			0.61		0.49

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.855
r_dihedral_angle_2_deg	36.204
r_dihedral_angle_4_deg	21.611
r_sphericity_bonded	17.943
r_dihedral_angle_3_deg	12.907
r_rigid_bond_restr	6.955
r_dihedral_angle_1_deg	6.164
r_angle_refined_deg	2.184
r_angle_other_deg	2.168
r_chiral_restr	0.163

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	36.855
r_dihedral_angle_2_deg	36.204
r_dihedral_angle_4_deg	21.611
r_sphericity_bonded	17.943
r_dihedral_angle_3_deg	12.907
r_rigid_bond_restr	6.955
r_dihedral_angle_1_deg	6.164
r_angle_refined_deg	2.184
r_angle_other_deg	2.168
r_chiral_restr	0.163
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2232
Nucleic Acid Atoms
Solvent Atoms	489
Heterogen Atoms	107

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
REFMAC	refinement
XDS	data reduction
XSCALE	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.