24SP

Human KRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AP6296

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SPRING-8 BEAMLINE BL45XU
Synchrotron site	SPring-8
Beamline	BL45XU
Temperature [K]	100
Detector technology	PIXEL
Collection date	2024-11-06
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.99999
Spacegroup name	P 1
Unit cell lengths	41.430, 45.025, 57.779
Unit cell angles	87.21, 89.83, 65.79

Refinement procedure

Resolution	57.700 - 1.450
R-factor	0.1944
Rwork	0.193
R-free	0.22480
Structure solution method	MOLECULAR REPLACEMENT
Data reduction software	XDS (Jan 31, 2020)
Data scaling software	Aimless (0.7.15)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.21.2_5419)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	57.700	57.700	1.774
High resolution limit [Å]	1.445	5.076	1.445
Rmerge	0.072	0.041	0.509
Rmeas	0.102	0.057	0.715
Rpim	0.071	0.040	0.502
Total number of observations	58900	3013	3014
Number of reflections	31129	1556	1556
<I/σ(I)>	3.4	5.53	1.68
Completeness [%]	83.5	99.3	33
Completeness (spherical) [%]	45.7	99.3	5.0
Completeness (ellipsoidal) [%]	83.5	99.3	33.0
Redundancy	1.89	1.94	1.94
CC(1/2)	0.988	0.992	0.600
Anomalous completeness (spherical)	30.2	85.8	1.4
Anomalous completeness	55.3	85.8	9.4
Anomalous redundancy	1.0	1.0	1.1
CC(ano)	0.000	0.000	0.000
|DANO|/σ(DANO)	0.4	0.3	0.5

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
1.714 Å	0.775, 0.775, 0.775
2.153 Å	-0.397, -0.397, -0.397
1.512 Å	-0.492, -0.492, -0.492
Criteria used in determination of diffraction limits	local <I/sigmaI> ≥ 1.2

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.2M Magnesium chloride, 0.1M Tris (pH 8.5), 25.0% (w/v) Polyethylene glycol 3350