7THD

Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B52

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	NSLS-II BEAMLINE 17-ID-1
Synchrotron site	NSLS-II
Beamline	17-ID-1
Temperature [K]	100
Detector technology	PIXEL
Collection date	2021-02-08
Detector	DECTRIS EIGER X 9M
Wavelength(s)	0.92011
Spacegroup name	P 2 21 21
Unit cell lengths	38.408, 67.032, 69.324
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	25.730 - 1.160
R-factor	0.1362
Rwork	0.136
R-free	0.15160
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2bit
RMSD bond length	0.011
RMSD bond angle	1.327
Data reduction software	XDS
Data scaling software	autoPROC
Phasing software	PHASER
Refinement software	PHENIX (1.17.1_3660)

Data quality characteristics

	Overall	Outer shell
Low resolution limit [Å]	25.730	1.190
High resolution limit [Å]	1.160	1.160
Rmerge	0.034	0.595
Rmeas	0.034	0.230
Rpim	0.024	0.163
Number of reflections	62319	4063
<I/σ(I)>	13.5	2.9
Completeness [%]	99.0	88.5
Redundancy	12.9	9.3
CC(1/2)	0.995	0.921

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	6	298	15% PEG 3350 0.5 M KH2PO4 1 mM NaCl Protein and inhibitor were mixed in ratio 1:2 1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor