9KPN | pdb_00009kpn

Crystal structure of KRAS-G12C in complex with Compound 20 (JAB-20)

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	5.3	277	0.1 M Sodium cacodylate, pH 5.3, 25% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
1.92	29.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.44	α = 90
b = 78.6	β = 90
c = 109.58	γ = 90

Symmetry
Space Group	P 2 21 21

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 PILATUS3 6M		2020-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.00000	SPring-8	BL45XU

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	1.29	44.954	99.9	0.182	0.987	11	11.7		75841

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	1.29	1.31			0.222	0.962	5.4

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	1.29	44.954	75770	3733	99.816	0.174	0.1726	0.1796	0.1931	0.1971	10.434

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]
-0.345			-0.111		0.456

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.343
r_dihedral_angle_4_deg	19.989
r_dihedral_angle_3_deg	12.247
r_dihedral_angle_1_deg	5.926
r_lrange_it	4.182
r_lrange_other	4.032
r_angle_refined_deg	1.516
r_scangle_it	1.494
r_scangle_other	1.493
r_angle_other_deg	1.398
r_mcangle_it	1.114
r_mcangle_other	1.114
r_scbond_it	0.925
r_scbond_other	0.923
r_mcbond_it	0.66
r_mcbond_other	0.66
r_symmetry_nbd_refined	0.248
r_nbd_other	0.219
r_symmetry_xyhbond_nbd_other	0.218
r_nbd_refined	0.212
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.159
r_ncsr_local_group_1	0.143
r_symmetry_xyhbond_nbd_refined	0.13
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.064
r_gen_planes_refined	0.009
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2662
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	148

Software

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