8BMY

Bacteroides thetaiotaomicron surface lipoprotein bound to cyanocobalamin

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	57.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.315	α = 90
b = 59.078	β = 103.865
c = 101.544	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 PILATUS3 6M		2019-03-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96858	Diamond	I24

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	59.08	99.4	0.108	0.147	0.099	0.988	6	3.5		97918

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	1.72	1.75			0.736	0.999	0.672	0.557		3.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3DSM	1.72	55.072	97856	4849	99.455	0.181	0.1787	0.19	0.2227	0.23	19.783

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]
0.363		0.455	0.09		-0.604

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.543
r_dihedral_angle_4_deg	20.191
r_dihedral_angle_3_deg	11.472
r_dihedral_angle_1_deg	7.815
r_lrange_it	4.094
r_lrange_other	3.622
r_scangle_it	2.961
r_scangle_other	2.936
r_scbond_it	2.429
r_scbond_other	2.417
r_mcangle_it	2.384
r_mcangle_other	2.384
r_mcbond_it	1.896
r_mcbond_other	1.891
r_angle_refined_deg	1.694
r_rigid_bond_restr	1.356
r_angle_other_deg	1.274
r_symmetry_nbd_refined	0.258
r_nbd_other	0.212
r_symmetry_nbd_other	0.179
r_nbd_refined	0.177
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.172
r_symmetry_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.074
r_ncsr_local_group_1	0.067
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5480
Nucleic Acid Atoms
Solvent Atoms	825
Heterogen Atoms	208

Software

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