6UM4

Crystal structure of malate dehydrogenase from Naegleria fowleri ATCC 30863

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	2018-03-01
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 1
Unit cell lengths	60.330, 137.480, 139.280
Unit cell angles	91.09, 90.00, 91.48

Refinement procedure

Resolution	44.230 - 2.050
R-factor	0.2108
Rwork	0.211
R-free	0.23240
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1bdm_A as per MorDa
RMSD bond length	0.007
RMSD bond angle	0.841
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MoRDa
Refinement software	PHENIX (1.17_3644)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	44.230	44.230	2.100
High resolution limit [Å]	2.050	9.170	2.050
Rmerge	0.085	0.028	0.512
Rmeas	0.108	0.035	0.650
Total number of observations	718188
Number of reflections	271476	2974	19937
<I/σ(I)>	8.18	23.4	2.01
Completeness [%]	96.7	94.5	96.1
Redundancy	2.645	2.553	2.656
CC(1/2)	0.997	0.998	0.869

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Microlytics MCSG1 screen, condition H11: 25% PEG 3350, 200mM NaCl, 100mM HEPES / NaOH pH 7.5: NafoA.00005.a.B1.PS38166 at 16.9mg/ml + 2mM NAD. Cryo: 15% EG: tray: 298888 h11: puck eqq6-5.