7LBN | pdb_00007lbn

X-ray crystal structure of the SARS-CoV-2 main protease with Calpain I Inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.2M sodium citrate, 15% PEG3350, 20mM HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.78	55.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.481	α = 90
b = 80.729	β = 114.36
c = 51.579	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	100	PIXEL	DECTRIS EIGER X 16M		2020-11-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE A1	1	CHESS	A1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.76	50	97	0.038	0.905	38.4	3.2		35055			23.88

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.76	1.79	72.4		0.295	0.905	3.9	2.4

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 (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	THROUGHOUT	6WTK	1.76	43.25	33044	2000	97.69	0.16125	0.15979	0.17	0.18546	0.2	RANDOM	33.246

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]
0.02		0.2	0.15		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.999
r_dihedral_angle_4_deg	14.56
r_dihedral_angle_3_deg	12.148
r_long_range_B_refined	7.759
r_long_range_B_other	7.675
r_dihedral_angle_1_deg	6.895
r_scangle_other	3.683
r_scbond_it	2.608
r_scbond_other	2.6
r_mcangle_it	2.371
r_mcangle_other	2.371
r_angle_refined_deg	1.576
r_mcbond_it	1.567
r_mcbond_other	1.566
r_angle_other_deg	1.472
r_chiral_restr	0.084
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2297
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	32

Software

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