8OWW | pdb_00008oww

B5-5 nanobody bound to SARS-CoV-2 spike RBD (Wuhan)

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7Z1C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Tris pH 8.5, PEG smear low Seeded from crystals grown in ammonium nitrate, PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.038	α = 90
b = 70.029	β = 90
c = 109.005	γ = 90

Symmetry
Space Group	P 2 21 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 EIGER2 XE 16M		2022-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.969	45.079	99.9	0.2	0.203	0.038	0.999	15.3	53.6		25155

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.97	2.02			7.33	7.458	1.373	0.461		55.5

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	1.969	45.079	25113	1264	99.861	0.183	0.1806	0.1805	0.2231	0.2231	51.534

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]
1.966			-1.465		-0.501

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.409
r_dihedral_angle_3_deg	15.112
r_lrange_it	9.923
r_lrange_other	9.921
r_dihedral_angle_2_deg	9.156
r_dihedral_angle_1_deg	7.695
r_scangle_it	7.684
r_scangle_other	7.682
r_mcangle_it	5.823
r_mcangle_other	5.822
r_scbond_it	5.513
r_scbond_other	5.511
r_mcbond_it	4.283
r_mcbond_other	4.282
r_angle_refined_deg	2.182
r_angle_other_deg	0.684
r_symmetry_xyhbond_nbd_refined	0.463
r_symmetry_nbd_refined	0.29
r_xyhbond_nbd_refined	0.223
r_nbd_refined	0.221
r_symmetry_nbd_other	0.21
r_nbd_other	0.204
r_nbtor_refined	0.197
r_symmetry_xyhbond_nbd_other	0.17
r_chiral_restr	0.095
r_symmetry_nbtor_other	0.095
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2496
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2.multiplex	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building
PARROT	phasing