8BMZ

Bacteroides thetaiotaomicron surface lipoprotein BT1954 bound to adenosylcobalamin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DSM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M Lithium sulphate, 0.1M Tris pH 8.5, 1.26 M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.93	58.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.723	α = 90
b = 58.709	β = 104.132
c = 101.894	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 EIGER X 16M		2021-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.89843	Diamond	I03

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	2.3	70.28	100	0.231	0.273	0.144	0.984	5.1	6.8		41492

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	2.3	2.38			0.957	1.142	0.617	0.696		6.5

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3DSM	2.3	70.276	41442	2001	99.906	0.225	0.2228	0.268	33.532

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]
1.812		2.426	-3.16		0.111

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.639
r_dihedral_angle_3_deg	14.595
r_dihedral_angle_2_deg	8.848
r_dihedral_angle_1_deg	8.379
r_lrange_it	4.915
r_lrange_other	4.915
r_dihedral_angle_other_2_deg	4.236
r_scangle_it	3.459
r_scangle_other	3.459
r_mcangle_other	2.968
r_mcangle_it	2.961
r_scbond_it	2.312
r_scbond_other	2.312
r_mcbond_it	1.961
r_mcbond_other	1.92
r_angle_refined_deg	1.79
r_angle_other_deg	0.669
r_symmetry_nbd_other	0.199
r_nbd_refined	0.187
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.171
r_nbd_other	0.154
r_symmetry_nbd_refined	0.094
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_refined	0.066
r_ncsr_local_group_1	0.059
r_symmetry_xyhbond_nbd_other	0.026
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5440
Nucleic Acid Atoms
Solvent Atoms	223
Heterogen Atoms	246

Software

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