7NKT

RBD domain of SARS-CoV2 in complex with neutralizing nanobody NM1226

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Z1Z	6Z1Z, 6XC4
experimental model	PDB	6XC4	6Z1Z, 6XC4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5	277	50mM K2HPO4, 20% (w/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.093	α = 90
b = 128.093	β = 90
c = 77.676	γ = 90

Symmetry
Space Group	I 41

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 PILATUS 2M		2020-12-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9999	SLS	X06DA

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	2.297	46.103	99.9	0.999	19.5	9.1		28115

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	2.297	2.44	99.6		0.484	1.4

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6Z1Z, 6XC4	2.3	46.103	28115	1687	99.908	0.187	0.1843	0.2239	59.942

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]
0.682			0.682		-1.364

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.612
r_dihedral_angle_4_deg	19.526
r_dihedral_angle_3_deg	15.138
r_lrange_other	8.578
r_lrange_it	8.57
r_dihedral_angle_1_deg	7.715
r_scangle_it	5.482
r_scangle_other	5.426
r_mcangle_other	5.264
r_mcangle_it	5.262
r_scbond_it	3.99
r_scbond_other	3.87
r_mcbond_it	3.653
r_mcbond_other	3.64
r_angle_refined_deg	1.463
r_angle_other_deg	1.262
r_symmetry_nbd_refined	0.223
r_nbd_other	0.207
r_nbd_refined	0.19
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.142
r_symmetry_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2503
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	40

Software

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