6YZ7

H11-D4, SARS-CoV-2 RBD, CR3022 ternary complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YLA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		298	The best crystals were grown in condition containing 0.1 M sodium citrate tribasic dihydrate, pH 5.0, 10% (w/v) Polyethylene glycol 6000.

Crystal Properties
Matthews coefficient	Solvent content
3.92	68.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 154.598	α = 90
b = 154.598	β = 90
c = 229.312	γ = 90

Symmetry
Space Group	P 41 2 2

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 6M-F		2020-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.978	Diamond	I03

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	3.29	128.187	98	0.094	0.994	4.9	78		40954

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.29	3.35			4.094	0.369

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	6YLA	3.3	128.187	40954	1939	96.292	0.239	0.2377	0.2688	144.159

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]
-1.97			-1.97		3.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.684
r_dihedral_angle_3_deg	17.533
r_dihedral_angle_4_deg	14.96
r_dihedral_angle_1_deg	7.668
r_lrange_it	4.952
r_lrange_other	4.951
r_mcangle_it	2.879
r_mcangle_other	2.879
r_scangle_it	2.857
r_scangle_other	2.857
r_mcbond_other	1.679
r_mcbond_it	1.678
r_scbond_it	1.6
r_scbond_other	1.6
r_angle_refined_deg	1.39
r_angle_other_deg	1.126
r_symmetry_xyhbond_nbd_other	0.32
r_nbd_other	0.237
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.206
r_symmetry_nbd_other	0.179
r_nbtor_refined	0.169
r_xyhbond_nbd_refined	0.164
r_symmetry_nbtor_other	0.073
r_ncsr_local_group_2	0.063
r_chiral_restr	0.049
r_ncsr_local_group_1	0.046
r_ncsr_local_group_3	0.042
r_ncsr_local_group_4	0.014
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11686
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	28

Software

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