8RKG

Crystal structure of tetrameric collagenase-cleaved Xenopus ZP2-N2N3 (cleaved xZP2-N2N3)

This is a non-PDB format compatible entry.

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	ESRF BEAMLINE ID30B
Synchrotron site	ESRF
Beamline	ID30B
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-06-22
Detector	DECTRIS PILATUS3 6M
Wavelength(s)	1.77120
Spacegroup name	P 1 21 1
Unit cell lengths	88.210, 70.310, 149.860
Unit cell angles	90.00, 90.04, 90.00

Refinement procedure

Resolution	38.000 - 2.900
R-factor	0.2176
Rwork	0.212
R-free	0.24680
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	AlphaFold model
RMSD bond length	0.004
RMSD bond angle	0.670
Data reduction software	XDS (Feb 5, 2021 BUILT=20210323)
Data scaling software	XSCALE (Feb 5, 2021 BUILT=20210323)
Phasing software	PHASER (2.8.3)
Refinement software	PHENIX (1.19.2_4158+SVN)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	38.020	2.986
High resolution limit [Å]	2.900	2.900
Rmerge	0.233	1.110
Rmeas	0.280	1.353
Rpim	0.154	0.765
Number of reflections	40766	3372
<I/σ(I)>	4.9	1
Completeness [%]	99.1	99.6
Redundancy	3.2	2.9
CC(1/2)	0.960	0.320

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION	8.5	293	12.5% (v/v) MPD, 12.5% (v/v) PEG 1000, 12.5% (w/v) PEG 3350, 0.1 M Tris base/Bicine pH 8.5, 0.09 M NPS (nitrate, phosphate, sulfate; MD2-100-72, Molecular Dimensions).