9FS9

Self assembly domain of the surface layer protein of Viridibacillus arvi (aa 765-844)

X-RAY DIFFRACTION

---

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	7.5	293	JCSG+ eco, condition G10 0.15 M KBr, 30 % PEG 2000 MME 22 g/l protein in 25 mM HEPES pH 7.5, 150 mM NaCl 0.3 ul condition + 0.3 ul protein

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.017	α = 90
b = 35.049	β = 91.234
c = 68.017	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	Bruker PHOTON III		2024-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2+ 70 kV	1.3414

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	2.1	48.66	99.83	0.1155	0.994	9.3	6		19156			30.19

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	2.1	2.175			0.8077	0.589	1.4

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	FREE R-VALUE	2.1	48.658	19155	900	99.911	0.204	0.201	0.2599	37.483

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]
-0.828		-0.534	0.696		0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.745
r_dihedral_angle_3_deg	14.217
r_dihedral_angle_1_deg	7.972
r_lrange_it	6.243
r_lrange_other	6.17
r_scangle_it	3.338
r_scangle_other	3.337
r_mcangle_it	2.902
r_mcangle_other	2.902
r_scbond_it	2.167
r_scbond_other	2.166
r_mcbond_it	1.812
r_mcbond_other	1.809
r_angle_refined_deg	1.386
r_angle_other_deg	0.462
r_symmetry_xyhbond_nbd_refined	0.227
r_xyhbond_nbd_refined	0.217
r_nbd_refined	0.213
r_nbd_other	0.201
r_symmetry_nbd_other	0.187
r_symmetry_nbd_refined	0.171
r_nbtor_refined	0.165
r_ncsr_local_group_6	0.125
r_ncsr_local_group_2	0.121
r_ncsr_local_group_5	0.109
r_ncsr_local_group_1	0.099
r_ncsr_local_group_4	0.094
r_ncsr_local_group_3	0.09
r_symmetry_nbtor_other	0.083
r_symmetry_xyhbond_nbd_other	0.076
r_chiral_restr	0.056
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2535
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
DIALS	data reduction
pointless	data scaling
PHASER	phasing