4FWW

Crystal structure of the Sema-PSI extracellular domains of human RON receptor tyrosine kinase

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	19% PEG 4000, 0.1 M Sodium Acetate, pH 4.6, 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.4	α = 90
b = 73.3	β = 97.4
c = 87.9	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CCD	MARMOSAIC 300 mm CCD	mirrors	2010-02-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

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	1.85	19.32	90	0.069	10.46	2.8	57269	51510		-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	1.85	1.9	63.7		0.44	1.47	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2UZX chain B	1.85	19.32	51510	48882	2627	89.95	0.19311	0.19091	0.23245	RANDOM	51.634

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]
0.01		0.01			-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.483
r_dihedral_angle_4_deg	20.998
r_dihedral_angle_3_deg	15.249
r_dihedral_angle_1_deg	8.048
r_scangle_it	4.159
r_scbond_it	2.72
r_mcangle_it	1.69
r_angle_refined_deg	1.548
r_mcbond_it	1.032
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.307
r_nbd_refined	0.231
r_symmetry_vdw_refined	0.211
r_xyhbond_nbd_refined	0.192
r_chiral_restr	0.125
r_gen_planes_refined	0.013
r_bond_refined_d	0.012
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	3845
Nucleic Acid Atoms
Solvent Atoms	358
Heterogen Atoms	127

Software

Software
Software Name	Purpose
JBluIce-EPICS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling