24SR

Human NRAS 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	P 1 21 1
Unit cell lengths	62.873, 61.594, 83.712
Unit cell angles	90.00, 99.40, 90.00

Refinement procedure

Resolution	49.370 - 1.232
R-factor	0.1972
Rwork	0.196
R-free	0.21290
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]	82.588	82.588	1.385
High resolution limit [Å]	1.232	3.838	1.232
Rmerge	0.057	0.035	1.188
Rmeas	0.067	0.041	1.431
Rpim	0.036	0.022	0.786
Total number of observations	415374	21705	19069
Number of reflections	123736	6187	6187
<I/σ(I)>	7.71	17.95	1.52
Completeness [%]	91.2	99.9	48.5
Completeness (spherical) [%]	68.0	99.9	11.5
Completeness (ellipsoidal) [%]	91.2	99.9	48.5
Redundancy	3.36	3.51	3.08
CC(1/2)	0.997	0.994	0.402
Anomalous completeness (spherical)	62.1	98.8	9.4
Anomalous completeness	83.9	98.8	41.5
Anomalous redundancy	1.8	1.9	1.7
CC(ano)	0.087	0.022	-0.007
|DANO|/σ(DANO)	0.6	0.4	0.6

Diffraction limits	Principal axes of ellipsoid fitted to diffraction cut-off surface
1.259 Å	0.961, 0.961, 0.961
1.508 Å	0.000, 0.000, 0.000
1.330 Å	-0.276, -0.276, -0.276
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 Sodium phosphate monobasic, 20.0% (w/v) Polyethylene glycol 3350