Experiment: 7EWA

GDP-bound KRAS G12D in complex with TH-Z827

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4EPR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	8.5	297	0.2 M sodium acetate, 0.1 M Tris, pH 8.5, 26 % (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.691	α = 90
b = 102.793	β = 107.1
c = 56.395	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	100	CMOS	BRUKER PHOTON 100		2021-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	BRUKER METALJET	1.34138

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	2.25	50	100	0.0844	1	12.63	9.07		47529

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	2.25	2.28	100		0.3976	0.95	3.33	6.72

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4EPR	2.25	33.7	1.35	47529	3944	99.91	0.2076	0.203	0.2042	0.2584	0.2591	43.4692

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3902
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	169

Software

Software
Software Name	Purpose
PHENIX	refinement
SADABS	data scaling
PDB_EXTRACT	data extraction
SAINT	data reduction
PHASER	phasing