8CDC | pdb_00008cdc

Native 3CLpro from SARS-CoV-2 at 1.54 A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	20-60 mM ammonium acetate buffer at pH 7.0 and 20-30 % PEG4000 as a precipitant

Crystal Properties
Matthews coefficient	Solvent content
1.93	36.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.063	α = 90
b = 53.485	β = 102.995
c = 44.624	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		2022-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976240	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.54	55.6	100	0.05	0.054	0.03	0.999	15.3	6.6		38825

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	1.54	1.57	100		0.961	1.136	0.621	0.758	1.6

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	6YB7	1.54	43.519	38824	1916	99.915	0.188	0.1851	0.2	0.2391	0.25	25.543

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]
1.214		-0.946	0.72		-1.353

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.119
r_dihedral_angle_3_deg	15.44
r_dihedral_angle_2_deg	10.605
r_dihedral_angle_1_deg	7.618
r_lrange_other	7.19
r_lrange_it	7.174
r_scangle_it	5.569
r_scangle_other	5.567
r_mcangle_it	3.849
r_mcangle_other	3.849
r_scbond_it	3.779
r_scbond_other	3.778
r_mcbond_it	2.819
r_mcbond_other	2.81
r_angle_refined_deg	1.831
r_angle_other_deg	0.631
r_nbd_refined	0.244
r_symmetry_xyhbond_nbd_refined	0.215
r_nbd_other	0.201
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.185
r_symmetry_nbd_refined	0.138
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.049
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2358
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms

Software

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