7E6C | pdb_00007e6c

Crystal structure of L-cycloserine-bound form of cysteine desulfurase SufS C361A from Bacillus subtilis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5ZS9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	0.1 M Tris-HCl, 50 mM Lithium sulfate, 50%(v/v) PEG200

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.8	α = 90
b = 92.8	β = 90
c = 128.9	γ = 120

Symmetry
Space Group	P 31 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 EIGER X 16M		2020-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-17A	1.000	Photon Factory	BL-17A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.73	46.44	100	0.053	0.055	1	28.77	18.821		67513			39.397

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.83	100		0.798	0.82	0.913	3.72	18.451

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	5ZS9	1.73	46.44	64138	3376	99.99	0.1536	0.1524	0.15	0.1766	0.18	RANDOM	38.989

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]
0.05	0.03		0.05		-0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.543
r_dihedral_angle_4_deg	20.617
r_dihedral_angle_3_deg	14.123
r_dihedral_angle_1_deg	6.539
r_angle_refined_deg	2.462
r_chiral_restr	0.207
r_bond_refined_d	0.024
r_gen_planes_refined	0.015

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3224
Nucleic Acid Atoms
Solvent Atoms	250
Heterogen Atoms	117

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	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.