Experiment: 9WJ6

An integrated in silico-in vitro workflow for discovering high-affinity, selective antibodies to the KRAS(G12D)-MHC I complex

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ULK	HLA-C*08:02
experimental model	PDB	6ULK	Beta-2-microgulobulin
in silico model	AlphaFold		C8K10D5-1 Fab light chain
in silico model	AlphaFold		C8K10D5-1 Fab heavy chain

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295.15	1200mM NaH2PO4, 200mM (NH4)2SO4, 200mM Li2SO4, 100mM CAPS (pH 10.5)

Crystal Properties
Matthews coefficient	Solvent content
4.25	71.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 164.98	α = 90
b = 164.98	β = 90
c = 426.14	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295.15	PIXEL	DECTRIS EIGER X 9M		2025-03-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1.0	PAL/PLS	5C (4A)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	4.54	29.92	98.32	0.983	16.24	38.5		20332			118.67

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	4.54	4.7	91.91		0.917

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	FREE R-VALUE	4.54	29.92	1.35	20332	1999	98.83	0.281	0.2794	0.2782	0.2952	0.2957	168.14

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	22.8418
f_angle_d	0.6883
f_chiral_restr	0.0468
f_plane_restr	0.0043
f_bond_d	0.0033

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12934
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing