24SQ

Human HRAS 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	2024-10-16
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.99999
Spacegroup name	C 1 2 1
Unit cell lengths	135.935, 48.772, 65.546
Unit cell angles	90.00, 109.53, 90.00

Refinement procedure

Resolution	64.057 - 1.080
R-factor	0.1891
Rwork	0.188
R-free	0.20610
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]	64.057	64.057	1.199
High resolution limit [Å]	1.076	3.374	1.076
Rmerge	0.070	0.044	0.883
Rmeas	0.079	0.050	1.015
Rpim	0.036	0.022	0.492
Total number of observations	542086	28401	23867
Number of reflections	117556	5878	5878
<I/σ(I)>	10.2	29.56	1.6
Completeness [%]	93.5	100	68.5
Completeness (spherical) [%]	67.2	100.0	12.2
Completeness (ellipsoidal) [%]	93.5	100.0	68.5
Redundancy	4.61	4.83	4.06
CC(1/2)	0.997	0.996	0.639
Anomalous completeness (spherical)	65.3	99.9	11.5
Anomalous completeness	91.6	99.9	67.7
Anomalous redundancy	2.4	2.5	2.1
CC(ano)	-0.297	-0.389	-0.035
|DANO|/σ(DANO)	0.7	0.6	0.6

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
1.076 Å	0.998, 0.998, 0.998
1.323 Å	0.000, 0.000, 0.000
1.230 Å	0.067, 0.067, 0.067
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		293	0.2M Magnesium acetate, 20.0% (w/v) Polyethylene glycol 3350