9EWN | pdb_00009ewn

Mpro from SARS-CoV-2 with 4Q mutation

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	25% PEG 3350, 200 mM magnesium chloride hexahydrate, 0.1 M Bis-Tris pH 5.5

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.979	α = 90
b = 53.68	β = 100.819
c = 113.957	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	100	PIXEL	DECTRIS PILATUS3 S 6M		2022-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.11	48.402	99.1	0.137	0.162	0.086	0.996	7.6	6.7		15279

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.11	2.17			2.153	2.538	1.328	0.439		7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.113	48.402	15277	774	98.893	0.214	0.2102	0.22	0.2806	0.29	62.476

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]
-3.47		1.387	-2.225		4.813

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.315
r_lrange_it	14.194
r_lrange_other	14.192
r_dihedral_angle_6_deg	13.726
r_dihedral_angle_2_deg	11.568
r_scangle_it	8.957
r_scangle_other	8.955
r_dihedral_angle_1_deg	8.298
r_mcangle_it	7.339
r_mcangle_other	7.337
r_scbond_it	5.993
r_scbond_other	5.99
r_mcbond_it	5.238
r_mcbond_other	5.226
r_angle_refined_deg	1.652
r_angle_other_deg	0.685
r_nbd_refined	0.186
r_nbtor_refined	0.161
r_symmetry_nbd_other	0.152
r_xyhbond_nbd_refined	0.137
r_nbd_other	0.113
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbd_refined	0.11
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.069
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2323
Nucleic Acid Atoms
Solvent Atoms	26
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing
Aimless	data scaling