6EPN | pdb_00006epn

Ras guanine exchange factor SOS1 (Rem-cdc25) in complex with KRAS(G12C) and fragment screening hit F2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BKD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	Drops made from KRAS SOS1 complex (14.4 mg/ml in 5 mM Tris pH 7.5, 100mM NaCl) and reservoir solution (2.9 to 3.4 M sodium formate, 100 mM MES pH 6.5). Fragment soaked at 25 mM for 2.5 days using a 500 mM fragment stock solution in DMSO. Cryo buffer 0.1 M MES pH 6.5, 3.5 M sodium formate, 20 glycerol, 25 mM fragment.

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 149.99	α = 90
b = 149.99	β = 90
c = 201.07	γ = 90

Symmetry
Space Group	I 4 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2014-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.91841	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	CC (Half)	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	2.5	48.5	98.6	0.118	0.125	0.998	15.5	9		39446

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.65	98.3		0.862	0.912	0.751	2.6	9.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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	FOURIER SYNTHESIS	THROUGHOUT	1BKD	2.5	47.41	37472	1973	98.61	0.17916	0.17716	0.18	0.2185	0.22	RANDOM	53.29

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]
-0.12			-0.12		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.27
r_dihedral_angle_3_deg	16.705
r_dihedral_angle_4_deg	16.08
r_long_range_B_refined	10.388
r_long_range_B_other	10.388
r_scangle_other	7.833
r_mcangle_it	6.561
r_mcangle_other	6.561
r_dihedral_angle_1_deg	6.049
r_scbond_it	4.925
r_scbond_other	4.924
r_mcbond_it	4.101
r_mcbond_other	4.095
r_angle_refined_deg	1.359
r_angle_other_deg	0.968
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5193
Nucleic Acid Atoms
Solvent Atoms	287
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
REFMAC	phasing