7TDU | pdb_00007tdu

Joint X-ray/neutron structure of SARS-CoV-2 main protease (3CL Mpro) in complex with BBH-1

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7N8C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	287	20% PEG3350, 0.1 M Bis-Tris pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.02	α = 90
b = 81.217	β = 96.72
c = 88.825	γ = 90

Symmetry
Space Group	I 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	293	PIXEL	DECTRIS EIGER R 4M	OSMIC VARIMAX	2021-10-11	M	SINGLE WAVELENGTH
2	1	neutron	293	IMAGE PLATE	MAATEL	COLLIMATORS	2021-10-05	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54
2	NUCLEAR REACTOR	ILL BEAMLINE LADI III	3.0-4.0	ILL	LADI III

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.85	59.75	96.6	0.076						13.6	5.4		32013
2	2.2	44.04	78.7	0.161			0.094	0.986		7.9	3.1		15471

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.85	1.92		0.671						1.4	5.4
2	2.2	2.32		0.367			0.223	0.825		2.1	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	1.85	29.88			33147	28704	1415	86.6			0.197	0.18	0.21	0.2		33.86
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.2	29.9			19760	13060	652	66.1			0.237		0.257			33.86

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]

RMS Deviations
Key	Refinement Restraint Deviation
x_torsion_deg	29.4
x_torsion_deg	29.4
x_angle_deg	1.2
x_angle_deg	1.2
x_torsion_impr_deg	0.88
x_torsion_impr_deg	0.88
x_bond_d	0.011
x_bond_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2368
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	45

Software

Software
Software Name	Purpose
nCNS	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
PHASER	phasing
nCNS	phasing
LAUEGEN	data reduction
LSCALE	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.