6D3K | pdb_00006d3k

Crystal structure of unphosphorylated human PKR kinase domain in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UIU	PDB entry 3UIU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.1 M HEPES, pH 7.5, 6% v/v PEG400, 2.0 M ammonium sulfate, protein was complexed with AMP-PNP and Mg2+ prior to crystallization

Crystal Properties
Matthews coefficient	Solvent content
3.27	62.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.48	α = 90
b = 159.6	β = 90
c = 172.99	γ = 90

Symmetry
Space Group	C 2 2 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 325 mm CCD	Mirror: Flat bent collimating Rh coated mirror, toroidal focussing mirror	2016-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL14-1	0.979413	SSRL	BL14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	2.6	172.99	97.5	0.089	0.099	0.043	0.998	9.4	4.9		44360

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.7	98.7		1.49	1.661	0.716	0.666		4.8

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 (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 3UIU	2.6	172.99	42089	2245	97.16	0.212	0.209	0.2157	0.2655	0.2727	RANDOM	85.889

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]
3.53			-5.08		1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.366
r_dihedral_angle_3_deg	20.489
r_dihedral_angle_4_deg	18.727
r_dihedral_angle_1_deg	7.243
r_angle_refined_deg	1.804
r_angle_other_deg	1.048
r_chiral_restr	0.094
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6294
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	139

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction