9IMX | pdb_00009imx

Immune complex of HEV E2s and P1-5B nanobody

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3GGQ
experimental model	PDB	7KN5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		293	6% isopropanol, 0.1M sodium acetate pH 4.5, 20% PEG MME550

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.393	α = 90
b = 51.402	β = 92.74
c = 265.172	γ = 90

Symmetry
Space Group	P 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 EIGER X 9M		2024-06-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979	SSRF	BL02U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.2	66.22	98.6	0.314	0.12	0.929	4.9	6.9		70266

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	2.2	2.31	97.8		0.379

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	3GGQ,7KN5	2.2	66.22	68192	2000	85.35	0.27511	0.2168	0.2131	0.2452	0.2415	RANDOM	32.063

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]
4.77		-4.36	4.46		-9.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.372
r_dihedral_angle_2_deg	12.769
r_dihedral_angle_1_deg	8.585
r_long_range_B_refined	5.189
r_long_range_B_other	5.188
r_mcangle_it	4.308
r_mcangle_other	4.308
r_scangle_other	3.542
r_mcbond_it	3.106
r_mcbond_other	3.105
r_scbond_it	2.492
r_scbond_other	2.492
r_angle_refined_deg	1.64
r_angle_other_deg	0.541
r_chiral_restr	0.072
r_gen_planes_refined	0.01
r_bond_refined_d	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_dihedral_angle_4_deg
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	7272
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms

Software

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