8BGD | pdb_00008bgd

Structure of Mpro from SARS-CoV-2 in complex with FGA147

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	295	0.1 M TRIS-HCl at pH 8.5 containing 20% PEG 2000 MME and 10 mM NiCl2

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.721	α = 90
b = 62.661	β = 90
c = 106.128	γ = 90

Symmetry
Space Group	P 21 21 2

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 PILATUS 6M		2021-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.978948888602	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.62	41.246	99.4	0.999	21.94	12.9		38449

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	1.62	1.68	97.1		0.0594	0.99	12.8

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	FREE R-VALUE	7K3T	1.621	41.246	38448	1840	99.403	0.194	0.1914	0.2011	0.2439	0.2529	32.708

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]
-1.122			1.835		-0.713

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.542
r_dihedral_angle_3_deg	15.5
r_dihedral_angle_2_deg	9.683
r_lrange_it	7.507
r_lrange_other	7.493
r_dihedral_angle_1_deg	7.104
r_scangle_it	6.211
r_scangle_other	6.21
r_mcangle_it	4.322
r_mcangle_other	4.322
r_scbond_it	4.193
r_scbond_other	4.192
r_mcbond_it	3.047
r_mcbond_other	3.044
r_angle_refined_deg	1.86
r_symmetry_nbd_refined	1.041
r_angle_other_deg	1.037
r_nbd_other	0.572
r_symmetry_xyhbond_nbd_refined	0.233
r_nbd_refined	0.231
r_symmetry_nbd_other	0.217
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.017
r_gen_planes_other	0.013
r_gen_planes_refined	0.011
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2368
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing