Experiment: 3FYK

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A06	1A06,1ATP,1CDK,2PHK
experimental model	PDB	1ATP	1A06,1ATP,1CDK,2PHK
experimental model	PDB	1CDK	1A06,1ATP,1CDK,2PHK
experimental model	PDB	2PHK	1A06,1ATP,1CDK,2PHK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	MK-2 protein at 5 mg/ml equilibrated against a well solution of 1.6 - 2.0 M Sodium malonate at pH 5.4, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
4.54	72.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 254.598	α = 90
b = 254.598	β = 90
c = 254.598	γ = 90

Symmetry
Space Group	F 41 3 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		2005-03-02		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00	APS	17-ID

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	3.5	30	93.2	0.083	19.778	7.5		8772

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)
	3.5	3.62	95.1		0.352		6.9	860

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	1A06,1ATP,1CDK,2PHK	3.5	30	8772	424	93.07	0.267	0.265	0.296	RANDOM	98.046

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.322
r_dihedral_angle_3_deg	21.834
r_dihedral_angle_4_deg	21.426
r_dihedral_angle_1_deg	5.992
r_scangle_it	1.758
r_angle_refined_deg	1.397
r_mcangle_it	1.203
r_scbond_it	0.957
r_mcbond_it	0.652
r_chiral_restr	0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.322
r_dihedral_angle_3_deg	21.834
r_dihedral_angle_4_deg	21.426
r_dihedral_angle_1_deg	5.992
r_scangle_it	1.758
r_angle_refined_deg	1.397
r_mcangle_it	1.203
r_scbond_it	0.957
r_mcbond_it	0.652
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2298
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	19

Software

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

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.