3DFC | pdb_00003dfc

Crystal structure of a glycine-rich loop mutant of the death associated protein kinase catalytic domain with AMPPNP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JKS	PDB entry 1jks

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	0.2M lithium nitrate, 2.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.688	α = 90
b = 62.444	β = 90
c = 88.602	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	MARMOSAIC 300 mm CCD	Be-lenses	2008-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.9	50	100	0.08		7.2	21129	21129		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	100		0.605	3.2	7.3	2071

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 (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 1jks	1.9	30	19184	19184	1028	95.98	0.16793	0.16476	0.1652	0.23048	0.2311	RANDOM	24.481

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]
0.07			-0.03		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.807
r_dihedral_angle_3_deg	13.433
r_dihedral_angle_4_deg	12.815
r_dihedral_angle_1_deg	4.664
r_scangle_it	4.3
r_scbond_it	2.656
r_mcangle_it	1.81
r_angle_refined_deg	1.546
r_mcbond_it	1.14
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.224
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.125
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2274
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	31

Software

Software
Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing