3BRB | pdb_00003brb

Crystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with ADP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P0C	PDB entry 2P0C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	290	MER protein (38 mg/mL) was pre-incubated with 2.5 mM ATP and 10 mM MgCl2 for 3 hours at room temperature. Crystals were obtained at 290K against 29% PEG 400, 0.2M MgCl2, and 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.385	α = 90
b = 89.88	β = 103.09
c = 69.537	γ = 90

Symmetry
Space Group	P 1 21 1

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 270	Rh coated Si mirrors	2007-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91790	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	25.05	98.3	0.09	24.1	7.2	49802	49802		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.97	88.7		0.659	2.3929	5.2

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 (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 2P0C	1.9	25.05	49525	47038	2487	98.32	0.19469	0.19221	0.2	0.24	0.25	RANDOM	33.967

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]
6.06		0.38	-2.51		-3.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.761
r_dihedral_angle_4_deg	20.243
r_dihedral_angle_3_deg	15.047
r_dihedral_angle_1_deg	5.58
r_scangle_it	4.712
r_scbond_it	3.602
r_mcangle_it	2.686
r_mcbond_it	1.904
r_angle_refined_deg	1.511
r_nbtor_refined	0.306

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.761
r_dihedral_angle_4_deg	20.243
r_dihedral_angle_3_deg	15.047
r_dihedral_angle_1_deg	5.58
r_scangle_it	4.712
r_scbond_it	3.602
r_mcangle_it	2.686
r_mcbond_it	1.904
r_angle_refined_deg	1.511
r_nbtor_refined	0.306
r_nbd_refined	0.202
r_symmetry_vdw_refined	0.173
r_xyhbond_nbd_refined	0.137
r_symmetry_hbond_refined	0.121
r_chiral_restr	0.103
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4126
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	67

Software

Software
Software Name	Purpose
PHASER	phasing
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	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.