7NEO | pdb_00007neo

Crystal Structure of SARS-CoV-2 main protease (Nsp5) in complex with compound 15

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7B2J

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.75	293	100 nL protein (8.3 mg/mL, 50 mM Tris pH 8.0, 300 mM NaCl), 50 nL seeds, 450 nL reservoir (200 mM HEPES pH 7.75, 5% DMSO, 12.5% PEG4K). Soaking: 200 mM HEPES pH 7.75, 12 mM compound, 5% DMSO, 10% PEG300, 20% PEG3K, RT, 2 h.

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.572	α = 90
b = 53.822	β = 100.492
c = 114.768	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 16M		2020-12-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.976	MAX IV	BioMAX

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.64	48.67	99.9	0.065	0.079	0.045	0.998	11.3	5.6		65712

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.67	100		0.431	0.529	0.302	0.94	3.2	5.6

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7B2J	1.64	48.627	65694	3193	99.919	0.203	0.2012	0.21	0.2387	0.24	18.668

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]
-0.87		-0.586	-0.339		1.335

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.721
r_dihedral_angle_3_deg	12.878
r_dihedral_angle_4_deg	12.715
r_dihedral_angle_1_deg	7.291
r_lrange_it	5.518
r_lrange_other	5.483
r_scangle_it	3.954
r_scangle_other	3.954
r_scbond_it	2.634
r_scbond_other	2.633
r_mcangle_it	2.544
r_mcangle_other	2.543
r_mcbond_it	1.767
r_mcbond_other	1.767
r_angle_refined_deg	1.704
r_angle_other_deg	1.507
r_nbd_other	0.215
r_symmetry_xyhbond_nbd_refined	0.214
r_nbd_refined	0.208
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.168
r_symmetry_nbd_refined	0.103
r_chiral_restr	0.088
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4716
Nucleic Acid Atoms
Solvent Atoms	492
Heterogen Atoms	70

Software

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