7NPA | pdb_00007npa

Crystal structure of the Coenzyme F420-dependent sulfite reductase from Methanothermococcus thermolithotrophicus at 1.55-A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NP8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293.15	Fsr from Methanothermococcus thermolithotrophicus was crystallized anaerobically under yellow light at a concentration of 11 mg ml-1 in 25 mM Tris/HCl pH 7.6, 10% v/v glycerol, 2 mM dithiothreitol, 0.5 mM FAD and 0.0155 mM F420H2. 0.6 ul of sample was mixed with 0.6 ul reservoir solution. The reservoir solution contained 0.2 M Lithium sulfate, 0.1 M Bis-Tris, pH 5.5 and 25 % w/v Polyethylene glycol 3350. Crystals appeared after few days.

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.148	α = 102.28
b = 124.157	β = 95.71
c = 241.062	γ = 90.25

Symmetry
Space Group	P 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 2M-F		2020-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.00004	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.55	121.276	94.5	0.183	0.198	0.075	0.996	8.7	7		1396397

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.689	70.9		1.623	1.755	0.664	0.439	1.5	6.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7NP8	1.55	77.29	1.96	1396186	69210	75.51	0.1594	0.1588	0.16	0.1711	0.17	26.3738

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]

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	77290
Nucleic Acid Atoms
Solvent Atoms	10774
Heterogen Atoms	3554

Software

Software
Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
autoPROC	data reduction
autoPROC	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.