9FCT

BtuJ1 - Bacteroides thetaiotaomicron B12 scavenging protein

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	3.5	293	29% w/v PEG, 0.2M sodium citrate pH 3.5

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 148.891	α = 90
b = 51.416	β = 131.789
c = 108.757	γ = 90

Symmetry
Space Group	C 1 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 9M		2024-02-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	1.6	81.09	82	0.2	0.2	0.1	0.968	1.7	4.4		66258			13.12

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	1.6	1.7			0.381

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.603	81.09	66257	3429	82.048	0.19	0.1886	0.2132	20.543

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]
0.128		0.159	-1.048		0.245

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.039
r_dihedral_angle_3_deg	11.096
r_dihedral_angle_2_deg	9.459
r_dihedral_angle_1_deg	8.647
r_lrange_it	7.503
r_lrange_other	6.593
r_angle_refined_deg	2.351
r_scangle_it	2.295
r_scangle_other	2.294
r_mcangle_it	2.044
r_mcangle_other	2.044
r_angle_other_deg	1.401
r_scbond_it	1.388
r_scbond_other	1.388
r_mcbond_it	1.172
r_mcbond_other	1.172
r_nbtor_refined	0.149
r_nbd_refined	0.142
r_symmetry_nbd_other	0.115
r_chiral_restr	0.111
r_nbd_other	0.111
r_symmetry_xyhbond_nbd_refined	0.1
r_symmetry_nbd_refined	0.083
r_xyhbond_nbd_refined	0.08
r_ncsr_local_group_1	0.066
r_symmetry_nbtor_other	0.059
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_gen_planes_other	0.01
r_bond_other_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3674
Nucleic Acid Atoms
Solvent Atoms	497
Heterogen Atoms	186

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
STARANISO	data scaling
PHASER	phasing