5ODH

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus soaked with heterodisulfide for 3.5 minutes

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ODC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	294	All crystallization was performed in an anaerobic chamber (95% N2/5% H2) with anoxic solution using the sitting drop method (96-well 2-drop MRC Crystallization Plates in polystyrene, Molecular Dimensions, Suffolk, UK). The crystallization reservoir contained 100 mM Tris/HCl, pH 8.5, 3% (v/v) DMSO, 30% (w/v) polyethylene glycol 4000, and 200 mM Na acetate trihydrate. Crystallization drop contained 1 ul HdrABC-MvhAGD at 25 mg/ml premixed with 2 mM FAD and 1 ul of precipitant. The crystals appeared after 1-2 weeks in this condition. The cryo-cool trapping experiment was performed as following: crystals were soaked for 3min30sec in the crystallization solution supplemented with 66 mM CoM-S-S-CoB. The crystal was cryo-protected by a soak in the crystallization solution supplemented by 30% glycerol and 10 mM CoM-S-S-CoB.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 366.381	α = 90
b = 97.104	β = 108.43
c = 133.974	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2016-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.97916	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.2	48.552	99.8	0.141	0.073	0.992	8.4	4.8		225651

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	99.5		0.435	0.237	0.451		4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5ODC	2.2	48.552	1.34	225648	11273	99.81	0.2154	0.2138	0.2447	40.4

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.043
f_angle_d	1.527
f_chiral_restr	0.148
f_bond_d	0.006
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	31029
Nucleic Acid Atoms
Solvent Atoms	610
Heterogen Atoms	469

Software

Software
Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.