7B27

RBD domain SARS-CoV2 in complex with neutralizing nanobody NM1230

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.9	293	200 mM MgCl2, 20% (w/v) PEG 3350, pH 5.9

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.29	α = 90
b = 63.29	β = 90
c = 411.91	γ = 90

Symmetry
Space Group	P 43 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	90	PIXEL	DECTRIS EIGER X 16M		2020-10-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.999998	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	2.9	46.5	93.5	0.207	0.998	7.8	6.06		18493			61

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.98	95.7		1.86	0.662	1.15

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	6XC4, 6Z1Z	2.902	30.002	18475	1293	93.44	0.269	0.2661	0.3051	67.189

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]
4.256			4.256		-8.511

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.602
r_dihedral_angle_3_deg	19.805
r_dihedral_angle_4_deg	17.164
r_lrange_it	6.835
r_lrange_other	6.832
r_mcangle_it	4.561
r_mcangle_other	4.56
r_dihedral_angle_1_deg	4.015
r_scangle_it	3.86
r_scangle_other	3.859
r_mcbond_it	2.695
r_mcbond_other	2.691
r_scbond_it	2.232
r_scbond_other	2.231
r_angle_refined_deg	1.217
r_angle_other_deg	1.047
r_symmetry_xyhbond_nbd_other	0.286
r_symmetry_nbd_refined	0.236
r_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.173
r_nbtor_refined	0.164
r_nbd_refined	0.162
r_nbd_other	0.159
r_symmetry_nbtor_other	0.071
r_symmetry_xyhbond_nbd_refined	0.054
r_chiral_restr	0.031
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4831
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	28

Software

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