3MPT | pdb_00003mpt

Crystal structure of P38 kinase in complex with a pyrrole-2-carboxamide inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WFC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	See publication for details , pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.376	α = 90
b = 85.859	β = 90
c = 124.463	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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2005-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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	1.89	62.23	93.8	0.138	7.9	5.66		37532			18.1

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)
	1.89	1.95	90.8		0.446	3.5	5.53	3573

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	1wfc	1.89	20	37456	1869	100	0.239	0.236	0.24	0.298	0.3	RANDOM	31.085

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]
-0.51			-0.35		0.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.252
r_dihedral_angle_4_deg	18.411
r_dihedral_angle_3_deg	14.038
r_scangle_it	4.552
r_dihedral_angle_1_deg	4.433
r_scbond_it	3.118
r_mcangle_it	2.166
r_angle_refined_deg	1.511
r_mcbond_it	1.183
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.252
r_dihedral_angle_4_deg	18.411
r_dihedral_angle_3_deg	14.038
r_scangle_it	4.552
r_dihedral_angle_1_deg	4.433
r_scbond_it	3.118
r_mcangle_it	2.166
r_angle_refined_deg	1.511
r_mcbond_it	1.183
r_chiral_restr	0.097
r_bond_refined_d	0.013
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2801
Nucleic Acid Atoms
Solvent Atoms	316
Heterogen Atoms	41

Software

Software
Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
d*TREK	data reduction
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.