7LMI

SARS-CoV-1 3CLPro in complex with N-(4-(1H-pyrazol-4-yl)phenyl)-2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(thiophen-3-ylmethyl)acetamide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3VB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	295	10% PEG 6000, 0.1M MES, 1mM DTT, 1mM EDTA, 3% DMSO, 10% Glycerol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.508	α = 90
b = 82.109	β = 104.657
c = 53.384	γ = 90

Symmetry
Space Group	C 1 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	80	CCD	RAYONIX MX-300		2020-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.978	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.707	32.359	99.75	0.054	2.59	6.4		48877

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	1.707	1.77			0.3218

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	NONE	3vb3	1.707	32.34	48877	2450	99.291	0.17	0.1674	0.2156	33.653

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]
-0.345		0.357	0.949		-0.696

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.735
r_dihedral_angle_4_deg	19.963
r_dihedral_angle_3_deg	15.086
r_dihedral_angle_1_deg	7.752
r_scangle_it	6.673
r_scangle_other	6.671
r_lrange_it	6.249
r_lrange_other	6.224
r_scbond_it	6.155
r_scbond_other	6.153
r_rigid_bond_restr	4.832
r_mcangle_other	4.492
r_mcangle_it	4.47
r_mcbond_it	4.015
r_mcbond_other	3.949
r_angle_refined_deg	1.959
r_angle_other_deg	1.502
r_nbd_other	0.248
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.203
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.106
r_chiral_restr	0.104
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.079
r_bond_refined_d	0.016
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2370
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing