8Q4K

Crystal structure of Borrelia burgdorferi BB0158

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, SITTING DROP	4.6	294	0.2 M ammonium sulfate 0.1 M sodium acetate (pH 4.6) 20% PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.063	α = 90
b = 81.774	β = 109.381
c = 80.801	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 S 6M		2022-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.918400	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.4	44.97	99.3	0.074	0.998	15	6.9		35959

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49			0.403	0.938	4

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	2.4	44.97	35949	1821	99.255	0.217	0.213	0.2973	48.838

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]
-0.002		0.004	-0.003		0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.938
r_dihedral_angle_3_deg	17.399
r_lrange_it	9.115
r_lrange_other	9.109
r_dihedral_angle_1_deg	7.818
r_scangle_it	6.417
r_scangle_other	6.417
r_mcangle_it	6.044
r_mcangle_other	6.044
r_scbond_it	4.24
r_scbond_other	4.206
r_mcbond_it	4.115
r_mcbond_other	4.113
r_angle_other_deg	2.287
r_angle_refined_deg	1.567
r_symmetry_nbd_refined	0.343
r_nbd_other	0.303
r_symmetry_nbd_other	0.222
r_nbd_refined	0.21
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.158
r_symmetry_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.064
r_bond_other_d	0.034
r_bond_refined_d	0.008
r_gen_planes_other	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6473
Nucleic Acid Atoms
Solvent Atoms	248
Heterogen Atoms	15

Software

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