9FYI | pdb_00009fyi

[4Fe-4S] Cluster-Containing L-Cysteine Desulfidase CyuA from Methanococcus maripaludis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q58431-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	298	ANAEROBY (<1.5 ppm O2) 13 % PEG 4000, 0.1 M NaCl, 0.1 M tri-sodium citrate dihydrate pH 5.5, 0.1 M LiSO4, 10 % glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.121	α = 90
b = 79.148	β = 90
c = 156.38	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 9M		2022-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980112	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.937	78.123	92.78	0.119	0.9956	11.519	10.91		15210

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.946	3.191	43.02		1.97	0.52	1.248	10.33

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.937	70.62	15210	723	82.6	0.2239	0.2219	0.2251	0.2614	0.2651	RANDOM	121.64

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]
1.3892			-0.9708		-0.4184

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.48
t_omega_torsion	2.32
t_angle_deg	0.89
t_bond_d	0.007
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_utility_distance
t_utility_angle

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.48
t_omega_torsion	2.32
t_angle_deg	0.89
t_bond_d	0.007
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_utility_distance
t_utility_angle
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5614
Nucleic Acid Atoms
Solvent Atoms	1
Heterogen Atoms	26

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHASES	phasing
BUSTER	refinement

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.