9EPL | pdb_00009epl

Mpro from SARS-CoV-2 with 298Q 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	20% PEG 3350, 0.1 mM benzamidine hydrochloride, 200 mM potassium formate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.26	α = 90
b = 53.1	β = 102.54
c = 44.63	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 PILATUS 6M		2022-10-06	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)	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	1.52	47.95	90	0.99	11.7	2.45		36271

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	1.52	1.61			0.343	0.55

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	1.8	47.944	21969	1099	90.259	0.152	0.1482	0.17	0.2276	0.24	20.731

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]
0.356		-2.196	2.736		-1.924

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.075
r_dihedral_angle_6_deg	15.366
r_dihedral_angle_2_deg	14.097
r_dihedral_angle_1_deg	7.968
r_rigid_bond_restr	6.062
r_lrange_it	4.344
r_lrange_other	4.28
r_scangle_it	3.509
r_scangle_other	3.283
r_mcangle_it	2.945
r_mcangle_other	2.944
r_scbond_it	2.722
r_scbond_other	2.552
r_mcbond_it	2.194
r_mcbond_other	2.194
r_angle_refined_deg	2.107
r_angle_other_deg	0.999
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.175
r_nbtor_refined	0.166
r_symmetry_nbd_other	0.154
r_nbd_other	0.128
r_symmetry_xyhbond_nbd_refined	0.119
r_chiral_restr	0.111
r_symmetry_nbd_refined	0.105
r_symmetry_nbtor_other	0.072
r_bond_refined_d	0.015
r_gen_planes_refined	0.014
r_bond_other_d	0.006
r_gen_planes_other	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2321
Nucleic Acid Atoms
Solvent Atoms	175
Heterogen Atoms	21

Software

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