9T2W | pdb_00009t2w

YdhG-like domain-containing protein (Frataxin) from Listeria monocytogenes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.3	295.15	2.5 mg/mL protein, 0.1 M MES. 10% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.974	α = 90
b = 51.296	β = 107.172
c = 60.583	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	PIXEL	DECTRIS EIGER2 S 9M		2023-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8731	ESRF	ID30B

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	1.72	57.88	99.9	0.173	0.188	0.072	0.966	6.9	6.8		27261			26

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	1.722	1.752	99		3.009	3.297	1.33	0.362	1.4	6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.75	57.88	26124	1296	99.752	0.182	0.1804	0.1821	0.2223	0.2241	RANDOM	30.7

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]
-1.986		-0.47	1.742		0.449

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.873
r_dihedral_angle_6_deg	13.682
r_dihedral_angle_2_deg	12.66
r_lrange_it	9.619
r_scangle_it	8.817
r_scbond_it	6.153
r_dihedral_angle_1_deg	5.687
r_mcangle_it	4.412
r_mcbond_it	3.46
r_angle_refined_deg	2.469
r_nbtor_refined	0.332
r_symmetry_nbd_refined	0.266
r_nbd_refined	0.222
r_symmetry_xyhbond_nbd_refined	0.211
r_chiral_restr	0.141
r_xyhbond_nbd_refined	0.139
r_ncsr_local_group_1	0.128
r_bond_refined_d	0.014
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1989
Nucleic Acid Atoms
Solvent Atoms	130
Heterogen Atoms	33

Software

Software
Software Name	Purpose
Aimless	data scaling
gemmi	data extraction
REFMAC	refinement
PHASER	phasing
Coot	model building
XDS	data reduction