8STN | pdb_00008stn

Crystal structure of KRAS-G12D/G75A mutant, GDP-bound

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5US4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.2 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.133	α = 90
b = 85.133	β = 90
c = 41.929	γ = 120

Symmetry
Space Group	P 3

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 16M		2022-12-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9791	APS	24-ID-E

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	73.73	99.7	0.11599999999999999	0.129	0.991	8.52	5.13		22917

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05			0.997	1.11	0.41700000000000004

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 (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	2.03	73.73	20732	1102	99.34	0.16117	0.15997	0.17	0.18261	0.19	RANDOM	40.642

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]
-6.06			-6.06		12.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.674
r_dihedral_angle_2_deg	12.63
r_long_range_B_refined	7.84
r_dihedral_angle_1_deg	6.607
r_mcangle_it	4.249
r_scbond_it	2.859
r_mcbond_it	2.826
r_angle_refined_deg	1.2
r_chiral_restr	0.091
r_gen_planes_refined	0.006
r_bond_refined_d	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2585
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	61

Software

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