7TH1

Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B3

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-2
Synchrotron site	NSLS-II
Beamline	17-ID-2
Temperature [K]	100
Detector technology	PIXEL
Collection date	2019-04-30
Detector	DECTRIS EIGER X 16M
Wavelength(s)	0.97933
Spacegroup name	P 21 21 21
Unit cell lengths	40.279, 60.265, 66.592
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	44.680 - 1.520
R-factor	0.17
Rwork	0.169
R-free	0.18860
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2bit
RMSD bond length	0.008
RMSD bond angle	1.299
Data reduction software	XDS
Phasing software	PHASER
Refinement software	PHENIX (1.17.1_3660)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	44.684	1.549
High resolution limit [Å]	1.520	1.520
Rmerge	0.165	1.607
Rmeas	0.173	1.671
Rpim	0.050	0.456
Number of reflections	25507	1301
<I/σ(I)>	9.1	3.2
Completeness [%]	99.9	100
Redundancy	11.9	13.1
CC(1/2)	0.996	0.911

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	28% PEG 3350 0.5 M KH2PO4 Protein and inhibitor were mixed in ratio 1:3 1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor