4DSO

Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.2 uL + 0.2 uL drops containing 40 mg/mL KRas, 0.1 M TrisCl, 25% polyethylene glycol 4000, 0.2 M NaOAc, 2% benzamidine-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.374	α = 90
b = 79.374	β = 90
c = 77.749	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	MARMOSAIC 325 mm CCD	Side scattering bent cube-root I-beam single crystal; asymmetric cut 4.965 degs	2009-01-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.97945	SSRL	BL11-1

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	1.85	30	98.7	0.059	18.1	5.3		14782	1	1

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	1.85	1.99	82.2		0.158	7.4	4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.85	25.92	15563	14782	781	99.84	0.17211	0.17022	0.20705	RANDOM	39.076

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]
-0.41	-0.2		-0.41		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.387
r_dihedral_angle_4_deg	20.783
r_dihedral_angle_3_deg	14.615
r_dihedral_angle_1_deg	7.5
r_scangle_it	2.88
r_scbond_it	2.084
r_angle_refined_deg	2.066
r_mcangle_it	1.358
r_mcbond_it	1.2
r_angle_other_deg	0.953
r_symmetry_hbond_refined	0.498
r_symmetry_vdw_other	0.308
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.227
r_nbd_other	0.214
r_mcbond_other	0.211
r_xyhbond_nbd_refined	0.204
r_nbtor_refined	0.178
r_metal_ion_refined	0.105
r_chiral_restr	0.088
r_nbtor_other	0.086
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.005
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1417
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	48

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling