8OWT | pdb_00008owt

SARS-CoV-2 spike RBD with A8 and H3 nanobodies bound

X-RAY DIFFRACTION

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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	NaCl, potassium citrate pH 4.2, PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.609	α = 90
b = 97.197	β = 90
c = 117.583	γ = 90

Symmetry
Space Group	P 21 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		2021-03-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.14	58.78	100	0.088	0.996	6.5	13.7		57917

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	2.14	2.18			0.324

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	2.37	58.78	42863	2056	99.991	0.214	0.2126	0.22	0.249	0.25	54.72

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]
-0.246			0.218		0.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.027
r_dihedral_angle_4_deg	14.816
r_dihedral_angle_3_deg	13.613
r_dihedral_angle_1_deg	6.771
r_lrange_it	3.921
r_lrange_other	3.913
r_scangle_it	2.249
r_scangle_other	2.249
r_mcangle_it	1.85
r_mcangle_other	1.85
r_scbond_it	1.382
r_scbond_other	1.335
r_angle_refined_deg	1.241
r_mcbond_it	1.142
r_mcbond_other	1.142
r_angle_other_deg	1.119
r_nbd_other	0.188
r_nbd_refined	0.174
r_nbtor_refined	0.166
r_symmetry_nbd_other	0.164
r_symmetry_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.127
r_xyhbond_nbd_refined	0.121
r_ncsr_local_group_1	0.088
r_ncsr_local_group_2	0.073
r_ncsr_local_group_3	0.071
r_symmetry_nbtor_other	0.068
r_chiral_restr	0.042
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6960
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
DIALS	data scaling
PHASER	phasing
Coot	model building