3D83

Crystal structure of P38 kinase in complex with a biphenyl amide inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	Authors suggest to see publication for details, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.24	α = 90
b = 86.523	β = 90
c = 127.108	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	100	CCD	ADSC QUANTUM 4		2001-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87000	SRS	PX9.6

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	1.9	35	82.4	0.053	12.9			34124			25.7

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	1.9	1.97	72.2		0.524	1.7		2939

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	FOURIER SYNTHESIS	THROUGHOUT	PDB entry 1WFC	1.9	20	33850	1712	100	0.177	0.175	0.218	RANDOM	35.516

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]
0.34			-0.51		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.542
r_dihedral_angle_4_deg	18.378
r_dihedral_angle_3_deg	14.665
r_dihedral_angle_1_deg	13.368
r_scangle_it	4.436
r_scbond_it	3.148
r_mcangle_it	1.995
r_angle_refined_deg	1.378
r_mcbond_it	1.293
r_nbtor_refined	0.301
r_nbd_refined	0.205
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.178
r_xyhbond_nbd_refined	0.17
r_chiral_restr	0.094
r_bond_refined_d	0.017
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2819
Nucleic Acid Atoms
Solvent Atoms	431
Heterogen Atoms	41

Software

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