7LB7 | pdb_00007lb7

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

X-RAY DIFFRACTION - NEUTRON DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XQS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.6	287	18% PEG3350, 0.1 M Bis-Tris pH 6.6

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.558	α = 90
b = 55.691	β = 101.31
c = 48.808	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	293	PIXEL	DECTRIS EIGER R 4M		2020-10-20	M	SINGLE WAVELENGTH
2	1	neutron	293	AREA DETECTOR	ORNL ANGER CAMERA		2020-10-15	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418
2	SPALLATION SOURCE	ORNL Spallation Neutron Source BEAMLINE MANDI	2.0 - 4.16	ORNL Spallation Neutron Source	MANDI

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	2	54.21	96.3	0.082						13.9	4.2		19852
2	2.4	14.29	83.4	0.176						11.4	4.05		9566

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	2	2.05		0.544						1.9	4
2	2.4	2.49		0.336						3.1	2.68

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	2	40		2.5		19261	984	97.5			0.204	0.1975	0.225	0.2193	RANDOM	38.51
NEUTRON DIFFRACTION	MOLECULAR REPLACEMENT	2.4	14.92		2.5		9539	470	82.8			0.216		0.228		RANDOM

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
o_angle_deg	1.1
o_bond_d	0.009
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d
o_dihedral_angle_d_na
o_dihedral_angle_d_prot
o_improper_angle_d
o_improper_angle_d_na
o_improper_angle_d_prot
o_mcbond_it
o_mcangle_it
o_scbond_it
o_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2368
Nucleic Acid Atoms
Solvent Atoms	95
Heterogen Atoms	49

Software

Software
Software Name	Purpose
nCNS	refinement
PHASER	phasing
CrysalisPro	data reduction
CrysalisPro	data scaling
Mantid	data reduction
LAUENORM	data scaling