9KPM | pdb_00009kpm

Crystal structure of KRAS-G12C in complex with compound 16 (JAB-16)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6P8W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	277	0.2 M Magnesium Chloride, 0.1 M Tris pH 8.3, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.69	α = 90
b = 86.69	β = 90
c = 42.68	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	PIXEL	DECTRIS EIGER X 9M		2020-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.12713	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.41	43.383	99.7	0.075	0.999	25.1	13.6		35392

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.41	1.43			0.716	0.766	2.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.41	43.383	35329	1796	99.555	0.18	0.1792	0.1792	0.1936	0.194	12.698

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]
-0.266	-0.133		-0.266		0.863

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.274
r_dihedral_angle_4_deg	13.372
r_dihedral_angle_3_deg	11.184
r_dihedral_angle_1_deg	6.548
r_lrange_it	3.924
r_lrange_other	3.767
r_scangle_it	1.776
r_scangle_other	1.775
r_angle_refined_deg	1.438
r_mcangle_it	1.417
r_mcangle_other	1.417
r_angle_other_deg	1.37
r_scbond_other	1.112
r_scbond_it	1.111
r_mcbond_it	0.819
r_mcbond_other	0.816
r_nbd_refined	0.21
r_symmetry_nbd_other	0.175
r_nbtor_refined	0.168
r_symmetry_xyhbond_nbd_refined	0.165
r_nbd_other	0.14
r_xyhbond_nbd_refined	0.125
r_symmetry_nbd_refined	0.096
r_symmetry_nbtor_other	0.073
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1349
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	73

Software

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