3KGA | pdb_00003kga

Crystal structure of MAPKAP kinase 2 (MK2) complexed with a potent 3-aminopyrazole ATP site inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	298	0.1M BICINE, 1.3M SODIUM MALONATE, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.67	66.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.12	α = 90
b = 103.12	β = 90
c = 165.415	γ = 120

Symmetry
Space Group	P 63 2 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		2007-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99990	SLS	X10SA

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	2.55	30	99.8	0.108	17.1	7.7	17605	17605		-3	37.6

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)
	2.55	2.66	99.9		0.526	3.9	7.7	1967

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FOURIER SYNTHESIS	THROUGHOUT	2.55	29.3	16723	881	99.93	0.18274	0.18002	0.18	0.23459	0.23	RANDOM	35.071

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]
-1.16	-0.58		-1.16		1.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.172
r_dihedral_angle_3_deg	17.591
r_dihedral_angle_4_deg	15.435
r_scangle_it	7.081
r_dihedral_angle_1_deg	6.102
r_scbond_it	4.933
r_mcangle_it	3.243
r_mcbond_it	2.011
r_angle_refined_deg	1.503
r_nbtor_refined	0.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.172
r_dihedral_angle_3_deg	17.591
r_dihedral_angle_4_deg	15.435
r_scangle_it	7.081
r_dihedral_angle_1_deg	6.102
r_scbond_it	4.933
r_mcangle_it	3.243
r_mcbond_it	2.011
r_angle_refined_deg	1.503
r_nbtor_refined	0.332
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.221
r_symmetry_vdw_refined	0.215
r_xyhbond_nbd_refined	0.187
r_chiral_restr	0.093
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2333
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	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.