9YPM | pdb_00009ypm

MboA with Leu-Ala-Arg peptide substrate and two Fe(II) ions bound

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, HANGING DROP	4.6	298	MboA crystals were prepared via the hanging drop vapor diffusion method in an Coy anaerobic chamber with an atmosphere of < 5 ppm of O2. Hanging drops were prepared by combining equal volumes of MboA (9 mg/mL) protein solution, reservoir solution (0.6 M lithium sulfate and 0.1 M sodium acetate, pH 4.6), and 0.2 uL of a 1:1000 dilution microseed master stock generated from apo crystals for a total drop volume of 2.2 uL. The Fe(II) + substrate bound structure was prepared by incubating apo crystals with 0.4 uL of 100 mM LAR peptide and 100 mM Fe2+ in 0.1 M sodium acetate, pH 4.6 for two hours prior to looping. Crystals were cryoprotected with the addition of 0.75 uL of 40% glycerol in 0.1 M sodium acetate, pH 4.6 and flash frozen in LN2

Crystal Properties
Matthews coefficient	Solvent content
4.22	70.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.094	α = 90
b = 157.094	β = 90
c = 157.423	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS PILATUS3 S 6M		2025-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.11	ALS	8.3.1

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	2.45	90.76	100	0.192	0.199	0.053	0.999	18.1	26.38		72777

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	2.45	2.5	100		3.043	3.158	0.842	0.571	1.4	27.05

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.45	90.76	1.33	72681	3591	99.98	0.1642	0.1626	0.1632	0.1951	0.1955	59.45

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.8051
f_angle_d	0.5396
f_chiral_restr	0.0367
f_bond_d	0.007
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7344
Nucleic Acid Atoms
Solvent Atoms	270
Heterogen Atoms	423

Software

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