6W04

Crystal structure of HAD hydrolase, family IA, variant 3 from Entamoeba histolytica HM-1:IMSS

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	2020-02-05
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 63
Unit cell lengths	100.910, 100.910, 45.240
Unit cell angles	90.00, 90.00, 120.00

Refinement procedure

Resolution	33.030 - 1.950
R-factor	0.1629
Rwork	0.158
R-free	0.21070
Structure solution method	SAD
RMSD bond length	0.009
RMSD bond angle	0.890
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	PHASER
Refinement software	PHENIX (1.18rc1)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	50.000	50.000	2.000
High resolution limit [Å]	1.950	8.720	1.950
Rmerge	0.063	0.051	0.494
Rmeas	0.068	0.055	0.530
Number of reflections	19394	239	1413
<I/σ(I)>	18.53	34.13	3.8
Completeness [%]	100.0	98.4	100
Redundancy	7.521	6.469	7.568
CC(1/2)	0.998	0.996	0.900

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	24.5 mg/mL EnhiA.01283.a.AE1.PS38608 (labeled as BrabA.17285.c.AE2) in 3 mM magnesium chloride against MCSG1_A2-C2 optimization screen, condition g3 (200 mM ammonium sulfate, 26% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.4), cryoprotectant: 15% ethylene glycol + 3 mM magnesium chloride in two steps, tray: 314701g3, puck wrw2-2, for experimental phasing, a crystal from MCSG1_A2-C2 optimization screen, condition e7 (300 mM lithium sulfate, 24% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.0) was soaked for 20 seconds in 90% reservoir + 10% 5 M sodium iodide in ethylene glycol, followed by another 20-second soak in 80% reservoir + 20% 5 M sodium iodide in ethylene glycol, vitrified in liquid nitrogen, tray 314703e7, puck ynn3-8
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	24.5 mg/mL EnhiA.01283.a.AE1.PS38608 (labeled as BrabA.17285.c.AE2) in 3 mM magnesium chloride against MCSG1_A2-C2 optimization screen, condition g3 (200 mM ammonium sulfate, 26% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.4), cryoprotectant: 15% ethylene glycol + 3 mM magnesium chloride in two steps, tray: 314701g3, puck wrw2-2, for experimental phasing, a crystal from MCSG1_A2-C2 optimization screen, condition e7 (300 mM lithium sulfate, 24% w/v PEG3350, 100 mM Bis-Tris-HCl, pH 5.0) was soaked for 20 seconds in 90% reservoir + 10% 5 M sodium iodide in ethylene glycol, followed by another 20-second soak in 80% reservoir + 20% 5 M sodium iodide in ethylene glycol, vitrified in liquid nitrogen, tray 314703e7, puck ynn3-8