4LOP | pdb_00004lop

Structural basis of autoactivation of p38 alpha induced by TAB1 (Tetragonal crystal form)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QUE	PDB ENTRY 3QUE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277.15	20% PEG 3350, 0.2 M Na/K tartrate, 0.1 M Bis-Tris propane, pH 6.5, 10% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.54	α = 90
b = 86.54	β = 90
c = 226.92	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	PSI PILATUS 6M		2012-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9778	Diamond	I03

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	2.049	86.6	99.5	0.084	8.5	3.2	103494	103422			26.7

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)
1	2.049	2.16	97.1		0.422	2.1	2.5	14756

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 3QUE	2.049	86.55	2	103422	98138	5283	99.3	0.228	0.14995	0.14793	0.16	0.18753	0.19	RANDOM	32.418

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]
6.22			6.22		-12.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.758
r_dihedral_angle_4_deg	18.778
r_dihedral_angle_3_deg	13.864
r_dihedral_angle_1_deg	6.644
r_angle_refined_deg	1.576
r_angle_other_deg	1.012
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.758
r_dihedral_angle_4_deg	18.778
r_dihedral_angle_3_deg	13.864
r_dihedral_angle_1_deg	6.644
r_angle_refined_deg	1.576
r_angle_other_deg	1.012
r_chiral_restr	0.091
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11732
Nucleic Acid Atoms
Solvent Atoms	865
Heterogen Atoms	180

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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.