7OFU

Structure of SARS-CoV-2 Papain-like protease PLpro in complex with 3, 4-Dihydroxybenzoic acid, methyl ester

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7NFV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	Co-crystallization with the compounds was achieved mixing 0.2 uL of protein solution (22 mg/mL) in 50 mM TRIS buffer (pH 8.0) containing 1 mM TCEP and 150 mM NaCl with 0.1 uL of reservoir solution consisting of 1.0M NaH2PO4/1.0MKH2PO4, 100mM Tris_HCl pH=7.5. This growth solution was equilibrated by sitting drop vapor diffusion against 80 uL reservoir solution. Prior to crystallization 100 nL droplets of 10 mM compound solutions in DMSO were applied to the wells of SwissCI 96-well plates (2-well) and subsequently dried in vacuum.

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.391	α = 90
b = 82.391	β = 90
c = 134.132	γ = 120

Symmetry
Space Group	P 32 2 1

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		2020-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

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	1.72	48.92	99.954	1	16.66	10.6		56596

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	1.72	1.782			0.576		10.9

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	7nfv	1.72	48.868	56588	2834	99.954	0.176	0.1749	0.202	33.774

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]
-0.073	-0.037		-0.073		0.238

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.102
r_dihedral_angle_4_deg	17.491
r_dihedral_angle_3_deg	15.352
r_lrange_it	7.346
r_lrange_other	7.092
r_dihedral_angle_1_deg	6.36
r_scangle_it	5.45
r_scangle_other	5.365
r_scbond_it	3.708
r_scbond_other	3.564
r_mcangle_it	2.815
r_mcangle_other	2.814
r_mcbond_it	2.125
r_mcbond_other	2.1
r_angle_refined_deg	1.933
r_angle_other_deg	1.534
r_symmetry_nbd_refined	0.253
r_nbd_other	0.221
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.212
r_nbtor_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.178
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_other	0.13
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.085
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2502
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	46

Software

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