6ZH9

Ternary complex CR3022 H11-H4 and RBD (SARS-CoV-2)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	mixing 0.2 uL of the 18 mg/mL complex with 0.1 uL of the crystallization buffer containing 0.2 M Sodium acetate trihydrate, 0.1 M MES pH 6.0, 20 % w/v PEG 8000.

Crystal Properties
Matthews coefficient	Solvent content
4.22	70.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 156.411	α = 90
b = 156.411	β = 90
c = 116.205	γ = 90

Symmetry
Space Group	P 42 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	100	PIXEL	DECTRIS PILATUS 6M-F		2020-06-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.98	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.31	80.253	100	0.091	1	0.018	25.6		22105

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.31	3.4			3.9	0.77	0.3	0.5

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	6ZBY	3.31	80.243	22065	1088	99.964	0.263	0.2609	0.3052	134

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]
-1.696			-1.696		3.392

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.97
r_dihedral_angle_1_deg	21.543
r_dihedral_angle_other_3_deg	20.671
r_lrange_it	19.804
r_lrange_other	19.804
r_dihedral_angle_4_deg	17.991
r_dihedral_angle_3_deg	17.099
r_mcangle_it	12.289
r_mcangle_other	12.288
r_scangle_it	11.809
r_scangle_other	11.808
r_mcbond_it	7.791
r_mcbond_other	7.787
r_scbond_it	7.25
r_scbond_other	7.249
r_angle_refined_deg	1.626
r_angle_other_deg	1.228
r_symmetry_xyhbond_nbd_refined	0.266
r_nbd_other	0.254
r_symmetry_nbd_other	0.188
r_nbd_refined	0.185
r_symmetry_nbd_refined	0.179
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.143
r_symmetry_nbtor_other	0.077
r_xyhbond_nbd_other	0.074
r_chiral_restr	0.059
r_bond_refined_d	0.008
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	5856
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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