4EPT | pdb_00004ept

Discovery of Small Molecules that Bind to K-Ras and Inhibit Sos-mediated Activation

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LF5	pdb entry 1LF5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	30% PEG8000, 0.1 M MES, 0.2 M sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.055	α = 90
b = 93.055	β = 90
c = 37.202	γ = 120

Symmetry
Space Group	P 63

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	Bruker Platinum 135		2011-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

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	2	50	99.5	0.113	10.2	4.7	12685	12614		-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	2	2.03	99.7		0.28	4.1	2.8

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 1LF5	2	50	12685	11632	596	96.48	0.23157	0.22934	0.23	0.27436	0.27	RANDOM	20.261

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]
-0.17	-0.09		-0.17		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.708
r_dihedral_angle_4_deg	22.625
r_dihedral_angle_3_deg	17.125
r_dihedral_angle_1_deg	7.145
r_scangle_it	5.171
r_scbond_it	3.481
r_mcangle_it	2.248
r_angle_refined_deg	2.024
r_mcbond_it	1.261
r_chiral_restr	0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.708
r_dihedral_angle_4_deg	22.625
r_dihedral_angle_3_deg	17.125
r_dihedral_angle_1_deg	7.145
r_scangle_it	5.171
r_scbond_it	3.481
r_mcangle_it	2.248
r_angle_refined_deg	2.024
r_mcbond_it	1.261
r_chiral_restr	0.139
r_bond_refined_d	0.024
r_gen_planes_refined	0.01
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	1323
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	43

Software

Software
Software Name	Purpose
PROTEUM PLUS	data collection
MOLREP	phasing
REFMAC	refinement
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.