3BPR | pdb_00003bpr

Crystal structure of catalytic domain of the proto-oncogene tyrosine-protein kinase MER in complex with inhibitor C52

X-RAY DIFFRACTION

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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		8.5	287	Compound C52 (50 mM in DMSO) was added to 8 mg/ml MER protein to the final concentration of 2.5 mM. The mixture was rocked at 277 K overnight and further concentrated to about 35 mg/ml. Crystals were grown by mixing 2 microliters of MER inhibitor solution and 2 microliters of reservoir solution (100 mM Tris-HCl pH 8.5, 3.64 M NaCl) at 287 K using the hanging-drop vapor-diffusion method. Crystals were cryo-protected with a solution composed of glycerol, ethylene glycol, glucose, and fructose., VAPOR DIFFUSION, HANGING DROP, pH 8.50

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.001	α = 90
b = 91.702	β = 94.06
c = 120.745	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 210	MIRRORS	2007-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID		APS	17-ID

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	2.8	50	99	0.15	9.1	3.3		37537		-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)
	2.8	2.9	94		0.53	2.3	2.9

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	2.8	47.3	35338	35338	1889	98.73	0.275	0.27361	0.28	0.30134	0.31	RANDOM	42.487

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]
-4.24		1.07	-4.73		9.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.029
r_dihedral_angle_3_deg	18.727
r_dihedral_angle_4_deg	17.442
r_dihedral_angle_1_deg	5.649
r_scangle_it	1.787
r_scbond_it	1.261
r_angle_refined_deg	1.239
r_mcangle_it	0.794
r_mcbond_it	0.49
r_nbtor_refined	0.305
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.144
r_symmetry_vdw_refined	0.139
r_symmetry_hbond_refined	0.131
r_chiral_restr	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8073
Nucleic Acid Atoms
Solvent Atoms	131
Heterogen Atoms	99

Software

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