7UIA | pdb_00007uia

Crystal structure of BoNT/E receptor binding domain in complex with SV2 and VHH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FFZ	3FFZ, 5JLV, 6GLW
experimental model	PDB	5JLV	3FFZ, 5JLV, 6GLW
experimental model	PDB	6GLW	3FFZ, 5JLV, 6GLW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M HEPES, pH 7.5, 0.2 M potassium sulfate, 20% PEG 3350, and 5% (v/v) PEG 400

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140.742	α = 90
b = 172.335	β = 90
c = 137.162	γ = 90

Symmetry
Space Group	C 2 2 21

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		2019-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-E	0.9792	APS	24-ID-E

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	2.59	137.16	100	0.999	19.9	12.1		52103

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	2.59	2.67			0.894

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3FFZ, 5JLV, 6GLW	2.59	109.01	49418	2660	99.93	0.22711	0.22595	0.23	0.24897	0.25	RANDOM	51.741

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]
4.94			-2.89		-2.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.521
r_dihedral_angle_4_deg	17.692
r_dihedral_angle_3_deg	16.164
r_dihedral_angle_1_deg	6.188
r_long_range_B_refined	5.175
r_long_range_B_other	5.153
r_mcangle_it	3.617
r_mcangle_other	3.617
r_scangle_other	3.3
r_mcbond_it	2.25
r_mcbond_other	2.25
r_scbond_it	2.044
r_scbond_other	2.032
r_angle_other_deg	1.254
r_angle_refined_deg	1.128
r_chiral_restr	0.041
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10169
Nucleic Acid Atoms
Solvent Atoms	160
Heterogen Atoms	182

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing