9HMR | pdb_00009hmr

KRAS-G12V-D92C covalently bound to BI-1830

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8R7W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M BIS-TRIS propane pH 7.5, 10% ethylene glycol, 20% PEG 3350, 0.2 M sodium fluoride

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.871	α = 90
b = 116.558	β = 108.636
c = 68.642	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	193	PIXEL	DECTRIS EIGER2 X 16M		2023-05-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999905	SLS	X10SA

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	1.5	58.28	99.4	0.078	9.8	6.7		103561

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	1.5	1.53			1.042

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	39.155	103561	5060	99.371	0.207	0.2054	0.2092	0.2393	0.2414	RANDOM	28.417

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]
49.476		2.908	-14.031		-35.445

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	27.923
r_dihedral_angle_6_deg	17.089
r_scangle_it	16.853
r_rigid_bond_restr	15.357
r_dihedral_angle_2_deg	14.214
r_scbond_it	12.909
r_dihedral_angle_3_deg	12.699
r_mcangle_it	12.623
r_mcbond_it	9.975
r_dihedral_angle_1_deg	5.811
r_angle_refined_deg	1.928
r_nbtor_refined	0.311
r_symmetry_nbd_refined	0.226
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.21
r_symmetry_xyhbond_nbd_refined	0.165
r_chiral_restr	0.123
r_ncsr_local_group_6	0.098
r_ncsr_local_group_4	0.093
r_ncsr_local_group_3	0.088
r_ncsr_local_group_5	0.088
r_ncsr_local_group_1	0.085
r_ncsr_local_group_2	0.077
r_gen_planes_refined	0.017
r_bond_refined_d	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4939
Nucleic Acid Atoms
Solvent Atoms	374
Heterogen Atoms	216

Software

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