4Q75

Crystal structure of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1T3I	PDB ENTRY 1T3I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	microbatch under oil	7.5	278	20% PEG3000, 0.2M sodium chloride and 0.1M HEPES pH 7.5, microbatch under oil, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.567	α = 90
b = 68.205	β = 94.76
c = 87.066	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	ADSC QUANTUM 315r		2012-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.978542	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.709	45.853	95			97828	97823

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.71	1.8	75		0.187	3.5	2.6	11087

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 1T3I	1.709	45.853	1.34	97828	97823	4892	94.77	0.204	0.204	0.2025	0.2	0.2326	0.22	Scaling input intensities via French-Wilson Method

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]
-0.8666		-0.7462	-0.4169		1.2835

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.085
f_angle_d	1.127
f_chiral_restr	0.076
f_bond_d	0.007
f_plane_restr	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6444
Nucleic Acid Atoms
Solvent Atoms	854
Heterogen Atoms

Software

Software
Software Name	Purpose
Xnemo	data collection
MOLREP	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

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.