9DCL | pdb_00009dcl

[2Fe-2S] SufU from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-O53156

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	0.2 M calcium acetate hydrate, 0.1 M sodium cacodylate pH 6.5, 40% v/v PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.118	α = 90
b = 100.118	β = 90
c = 31.333	γ = 90

Symmetry
Space Group	I 4

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		2022-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.9537	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.95	35.42	100	0.995	7.8	27.3		11785

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.05	100		0.699

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	1.95	35.42	11605	578	99.983	0.18	0.1786	0.192	0.2099	0.221	Random	31.577

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]
-0.48			-0.48		0.961

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.978
r_dihedral_angle_other_3_deg	12.965
r_dihedral_angle_3_deg	12.242
r_dihedral_angle_2_deg	9.32
r_lrange_other	8.715
r_lrange_it	8.662
r_scangle_other	7.894
r_scangle_it	7.889
r_dihedral_angle_1_deg	5.72
r_scbond_other	5.088
r_scbond_it	5.073
r_mcangle_it	4.147
r_mcangle_other	4.145
r_mcbond_other	3.259
r_mcbond_it	3.258
r_angle_refined_deg	1.289
r_angle_other_deg	0.397
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.105
r_nbd_other	0.098
r_symmetry_xyhbond_nbd_refined	0.092
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.054
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1110
Nucleic Acid Atoms
Solvent Atoms	36
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing