9QBK | pdb_00009qbk

Bacillus Botulinum neurotoxin-like Protein 1 (BBP1)

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		291	MORPHEUS D6: 0.12 M, Alcohols mix, 0.1 M MOPS/HEPES-Na pH 7.6, 52.5% Precipitant mix 2

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 243.744	α = 90
b = 51.446	β = 115.394
c = 104.528	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 EIGER2 X 16M		2024-11-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.9763	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	37.931	99	0.985	9.4	6.7		29024

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	2.8	2.95			0.855

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	37.931	29017	1429	98.62	0.243	0.2401	0.2406	0.3012	0.2999	66.131

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]
-0.506		-0.134	-2.033		1.838

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.123
r_dihedral_angle_6_deg	15.252
r_dihedral_angle_1_deg	9.361
r_lrange_it	8.08
r_lrange_other	8.079
r_dihedral_angle_2_deg	6.55
r_mcangle_it	5.067
r_mcangle_other	5.066
r_scangle_it	5.028
r_scangle_other	5.028
r_scbond_it	3.149
r_scbond_other	3.149
r_mcbond_it	3.126
r_mcbond_other	3.126
r_angle_refined_deg	1.843
r_angle_other_deg	0.657
r_symmetry_nbd_refined	0.541
r_nbd_other	0.45
r_nbd_refined	0.258
r_symmetry_nbd_other	0.228
r_xyhbond_nbd_refined	0.227
r_nbtor_refined	0.199
r_symmetry_nbtor_other	0.099
r_symmetry_xyhbond_nbd_other	0.099
r_chiral_restr	0.083
r_bond_refined_d	0.007
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	5987
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	1

Software

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