3E92 | pdb_00003e92

Crystal Structure of P38 Kinase in Complex with A Biaryl Amide Inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	293	18-22% PEG 5000MME, 0.18M ammonium sulphate, 3-4% jeffamine, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.516	α = 90
b = 86.224	β = 90
c = 124.191	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	RIGAKU RAXIS IV++	MIRRORS	2002-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH2R	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	2	35	87.1	0.059	18.4			29459			34.3

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	2.07	69.8		0.554	1.9		2327

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	PDB ENTRY 1WFC	2	20	29392	1497	100	0.174	0.172	0.1764	0.216	0.2204	RANDOM	42.922

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]
0.67			-1.93		1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.933
r_dihedral_angle_4_deg	19.139
r_dihedral_angle_3_deg	12.81
r_dihedral_angle_1_deg	11.796
r_scangle_it	4.605
r_scbond_it	3.198
r_mcangle_it	2.219
r_angle_refined_deg	1.547
r_mcbond_it	1.33
r_nbtor_refined	0.306
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.184
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.109
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2816
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	50

Software

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