7LMJ | pdb_00007lmj

SARS-CoV-1 3CLPro in complex with 2-(1H-benzo[d][1,2,3]triazol-1-yl)-N-(3-chlorobenzyl)-N-(4-(2-oxo-1,2-dihydropyridin-3-yl)phenyl)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
3.37	63.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 107.539	α = 90
b = 82.712	β = 105.299
c = 53.2	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	1.686	32.356	99.5	0.029	17.06	7.4		50084

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.686	1.75			0.2421

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	NONE	3VB3	1.686	32.356	50084	2506	98.847	0.148	0.1456	0.16	0.1917	0.2	38.825

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]
-0.169		-0.239	0.531		-0.201

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.351
r_dihedral_angle_4_deg	16.714
r_dihedral_angle_3_deg	14.495
r_scangle_it	8.04
r_scangle_other	8.038
r_scbond_it	7.63
r_scbond_other	7.627
r_dihedral_angle_1_deg	7.368
r_lrange_it	7.288
r_lrange_other	7.143
r_rigid_bond_restr	5.374
r_mcangle_it	4.884
r_mcangle_other	4.883
r_mcbond_it	4.444
r_mcbond_other	4.444
r_angle_refined_deg	1.927
r_angle_other_deg	1.523
r_nbd_other	0.232
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.199
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.174
r_symmetry_xyhbond_nbd_refined	0.137
r_chiral_restr	0.103
r_symmetry_nbtor_other	0.082
r_bond_refined_d	0.016
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2371
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	66

Software

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