6TM3

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in a close conformation containing NADP+ and methylene-H4MPT

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	SLS BEAMLINE X10SA
Synchrotron site	SLS
Beamline	X10SA
Temperature [K]	100
Detector technology	PIXEL
Collection date	2018-02-04
Detector	DECTRIS PILATUS 6M-F
Wavelength(s)	1.00000
Spacegroup name	P 41 3 2
Unit cell lengths	125.754, 125.754, 125.754
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	41.918 - 1.080
R-factor	0.1135
Rwork	0.113
R-free	0.12700
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	1lu9
Data reduction software	XDS
Data scaling software	SCALA (3.3.22)
Phasing software	MOLREP
Refinement software	PHENIX (1.14_3260)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	88.922	41.918	1.140
High resolution limit [Å]	1.080	3.420	1.080
Rmerge		0.020	1.403
Rmeas	0.051	0.021	1.578
Rpim	0.016	0.007	0.705
Total number of observations	1439110	46109	95042
Number of reflections	143688	5001	20223
<I/σ(I)>	25.1	105.1	1.1
Completeness [%]	99.6	99.9	97.6
Redundancy	10	9.2	4.7

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8	281.15	The crystallized sample was 25 mg/ml MtdA supplemented with 2.5 mM methenyl-H4MPT, 2 mM NADPH in 25 mM Tris/HCl pH 7.5, 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol. 0.7 ul protein sample was mixed with 0.7 ul of the reservoir solution containing 30% w/v polyethylene glycol monomethyl ether 5000, 100 mM Tris pH 8.0 and 200 mM lithium sulfate.