3MH1

Mutagenesis of p38 MAP kinase establishes key roles of Phe169 in function and structural dynamics and reveals a novel DFG-out state

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	295	10-20% PEG 4000, 0.1 M cacodylic acid, 50 mM n-octyl-beta-D-glucoside, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.44	α = 90
b = 73.88	β = 90
c = 76.03	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	93	CCD	ADSC QUANTUM 4	Mirrors	2004-08-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	0.98	NSLS	X4A

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	2.2	40	78.2	0.12	0.094	7.5		21427	15280

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)
	2.2	2.37	83.4		0.397	0.388	2.5		3198

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	PDB ENTRY 1ZYJ	2.2	24.7	16691	1430	92.96	0.23511	0.23002	0.29583	RANDOM	26.122

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]
-0.43			-0.87		1.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.733
r_dihedral_angle_4_deg	21.499
r_dihedral_angle_3_deg	19.833
r_dihedral_angle_1_deg	6.617
r_scangle_it	4.148
r_scbond_it	2.634
r_mcangle_it	1.794
r_angle_refined_deg	1.712
r_mcbond_it	0.98
r_chiral_restr	0.121

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.733
r_dihedral_angle_4_deg	21.499
r_dihedral_angle_3_deg	19.833
r_dihedral_angle_1_deg	6.617
r_scangle_it	4.148
r_scbond_it	2.634
r_mcangle_it	1.794
r_angle_refined_deg	1.712
r_mcbond_it	0.98
r_chiral_restr	0.121
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2710
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.