7TGS

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

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	38.505, 57.879, 78.010
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	46.480 - 1.750
R-factor	0.1709
Rwork	0.170
R-free	0.18420
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	2bit
RMSD bond length	0.007
RMSD bond angle	0.986
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]	46.480	1.776
High resolution limit [Å]	1.750	1.750
Rmerge	0.136	1.195
Rmeas	0.142	0.142
Rpim	0.040	0.333
Number of reflections	17266	869
<I/σ(I)>	12.5	2.3
Completeness [%]	94.2	99.9
Redundancy	12.7	13.5
CC(1/2)	0.996	0.772

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, HANGING DROP	7.3	298	19% PEG 3350 0.5 M KH2PO4 1:3 ratio of protein to inhibitor 1 uL of protein:inhibitor complex was mixed with 1 uL of mother liquor