7L4A

Crystal Structure of Cytidylate kinase from Encephalitozoon cuniculi GB-M1 in complex with two CDP molecules

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2020-12-03
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 1 21 1
Unit cell lengths	48.520, 46.870, 53.830
Unit cell angles	90.00, 112.59, 90.00

Refinement procedure

Resolution	44.800 - 1.500
R-factor	0.1507
Rwork	0.148
R-free	0.19030
Structure solution method	SAD
RMSD bond length	0.008
RMSD bond angle	0.954
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.19rc4 4035)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	1.540
High resolution limit [Å]	1.500	6.710	1.500
Rmerge	0.042	0.026	0.448
Rmeas	0.049	0.031	0.538
Number of reflections	35784	425	2562
<I/σ(I)>	17.71	39.97	2.49
Completeness [%]	99.5	98.2	97
Redundancy	4.026	3.732	3.189
CC(1/2)	0.999	0.998	0.822

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	5.5	287	Optimization condition: 100mM BisTris pH 6, 200mM ammonium sulfate, 26% (w/V) PEG 3350: EucuA.01086.a.AE1.PS38633 at 56.56mg/ml + 5mM CTP + 5mM MgCl2: tray 318933 a2: cryo: 20% EG + ligands: puck akp1-5. For phasing, a crystal from MCSG1, condition D7 (20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: EncuA.01086.a.AE1.PS38636 at 28.28mg/ml, tray 315976 d7) was dipped for 20sec in a solution of 4ul half saturated NaI in ethylene glycol and reservoir and directly vitrified. This crystal form could not be reproduced.
1	VAPOR DIFFUSION, SITTING DROP	5.5	287	Optimization condition: 100mM BisTris pH 6, 200mM ammonium sulfate, 26% (w/V) PEG 3350: EucuA.01086.a.AE1.PS38633 at 56.56mg/ml + 5mM CTP + 5mM MgCl2: tray 318933 a2: cryo: 20% EG + ligands: puck akp1-5. For phasing, a crystal from MCSG1, condition D7 (20% (w/V) PEG 3000, 100mM sodium citrate tribasic / citric acid pH 5.5: EncuA.01086.a.AE1.PS38636 at 28.28mg/ml, tray 315976 d7) was dipped for 20sec in a solution of 4ul half saturated NaI in ethylene glycol and reservoir and directly vitrified. This crystal form could not be reproduced.