2P3G

Crystal structure of a pyrrolopyridine inhibitor bound to MAPKAP Kinase-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Structure of MAPKAP Kinase-2/AMP-PNP complex solved using ERK-2 as a starting model for molecular replacement

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	Protein solution (5 mg/ml) euqilibrated against 1.6 - 2.0 M sodium malonate at pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
4.5	72.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 253.941	α = 90
b = 253.941	β = 90
c = 253.941	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 QUANTUM 210		2005-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.0	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	3.7	20	99.5	0.051	0.051	11.6	7.4	7892	7853		-1	105

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.7	3.83	99.5		0.407	0.407	3.8	6.9	752

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	Structure of MAPKAP Kinase-2/AMP-PNP complex solved using ERK-2 as a starting model for molecular replacement	3.8	20	8020	7247	335	99.52	0.303	0.3	0.374	RANDOM	135.676

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	39.3
r_dihedral_angle_3_deg	22.36
r_dihedral_angle_4_deg	15.832
r_dihedral_angle_1_deg	7.15
r_scangle_it	1.632
r_angle_refined_deg	1.443
r_mcangle_it	1.331
r_scbond_it	0.907
r_mcbond_it	0.739
r_nbtor_refined	0.332
r_nbd_refined	0.264
r_symmetry_vdw_refined	0.204
r_xyhbond_nbd_refined	0.198
r_symmetry_hbond_refined	0.159
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2298
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	23

Software

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