8JJS

Human K-Ras G12D (GDP-bound) in complex with cyclic peptide inhibitor AP10343

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	PHOTON FACTORY BEAMLINE BL-1A
Synchrotron site	Photon Factory
Beamline	BL-1A
Temperature [K]	95
Detector technology	PIXEL
Collection date	2021-12-13
Detector	DECTRIS EIGER X 4M
Wavelength(s)	1.045000
Spacegroup name	P 61
Unit cell lengths	66.596, 66.596, 86.613
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	57.670 - 1.534
R-factor	0.2217
Rwork	0.221
R-free	0.24210
Structure solution method	MOLECULAR REPLACEMENT
RMSD bond length	0.007
RMSD bond angle	0.920
Data reduction software	XDS (Jan 31, 2020)
Data scaling software	Aimless (0.7.7)
Phasing software	PHASER
Refinement software	BUSTER (2.11.8)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	57.674	57.674	1.694
High resolution limit [Å]	1.534	4.808	1.534
Rmerge	0.104	0.036	1.536
Rmeas	0.106	0.037	1.593
Rpim	0.023	0.008	0.415
Total number of observations	442425	22624	14961
Number of reflections	21593	1080	1083
<I/σ(I)>	19.1	71.52	1.74
Completeness [%]	95.0	99.9	81.9
Completeness (spherical) [%]	66.2	99.9	12.9
Completeness (ellipsoidal) [%]	95.0	99.9	81.9
Redundancy	20.49	20.95	13.81
CC(1/2)	0.999	0.999	0.671
Anomalous completeness (spherical)	65.8	99.5	11.9
Anomalous completeness	94.4	99.5	73.8
Anomalous redundancy	10.4	11.0	7.4
CC(ano)	-0.329	-0.567	-0.024
|DANO|/σ(DANO)	0.7	0.8	0.7

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
1.856 Å	1.000, 1.000, 1.000
1.856 Å	0.000, 0.000, 0.000
1.499 Å	0.000, 0.000, 0.000

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP		293	2.0 M Ammonium sulfate, 25 %(v/v) Ethylene glycol as cryoprotectant