3GP0 | pdb_00003gp0

Crystal Structure of Human Mitogen Activated Protein Kinase 11 (p38 beta) in complex with Nilotinib

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GTN	ensemble comprising of 2GTN, 1P38, 1LEZ, 1BMK, 3FC1
experimental model	PDB	1P38	ensemble comprising of 2GTN, 1P38, 1LEZ, 1BMK, 3FC1
experimental model	PDB	1LEZ	ensemble comprising of 2GTN, 1P38, 1LEZ, 1BMK, 3FC1
experimental model	PDB	1BMK	ensemble comprising of 2GTN, 1P38, 1LEZ, 1BMK, 3FC1
experimental model	PDB	3FC1	ensemble comprising of 2GTN, 1P38, 1LEZ, 1BMK, 3FC1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	20% PEG 3350 0.1M citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.94	α = 90
b = 60.08	β = 90
c = 148.55	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		2009-01-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9253	Diamond	I04

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	1.9	49.51	100	0.117	0.117	12.6	7	28422	28422			19.8

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)
1	1.9	2	100		0.654	0.654	3.1	7.1	4091

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	ensemble comprising of 2GTN, 1P38, 1LEZ, 1BMK, 3FC1	1.9	49.51	28350	28361	1432	99.96	0.181	0.181	0.178	0.19	0.232	0.24	RANDOM	11.775

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]
-0.15			0.16		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.785
r_dihedral_angle_4_deg	18.2
r_dihedral_angle_3_deg	14.121
r_scangle_it	8.286
r_scbond_it	6.81
r_dihedral_angle_1_deg	5.697
r_mcangle_it	4.436
r_mcbond_it	3.261
r_angle_refined_deg	1.527
r_chiral_restr	0.108

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.785
r_dihedral_angle_4_deg	18.2
r_dihedral_angle_3_deg	14.121
r_scangle_it	8.286
r_scbond_it	6.81
r_dihedral_angle_1_deg	5.697
r_mcangle_it	4.436
r_mcbond_it	3.261
r_angle_refined_deg	1.527
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2643
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	44

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

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.