6Y2F | pdb_00006y2f

Crystal structure (monoclinic form) of the complex resulting from the reaction between SARS-CoV-2 (2019-nCoV) main protease and tert-butyl (1-((S)-1-(((S)-4-(benzylamino)-3,4-dioxo-1-((S)-2-oxopyrrolidin-3-yl)butan-2-yl)amino)-3-cyclopropyl-1-oxopropan-2-yl)-2-oxo-1,2-dihydropyridin-3-yl)carbamate (alpha-ketoamide 13b)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BX4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	10% PEG 200, 0.1 M bis-tris propane, pH 9.0, 18% PEG 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.085	α = 90
b = 80.926	β = 114.838
c = 51.659	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 PILATUS3 2M		2020-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9184	BESSY	14.2

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	1.95	43.369	100	0.076	0.083	0.032	0.999	15.5	6.8		26757

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	1.95	2.06	100		0.826	0.892	0.335	0.809		7

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2BX4	1.95	43.369	26755	1293	99.955	0.18	0.1779	0.19	0.2191	0.22	4.83	36.377

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]
1.854		-0.302	1.848		-2.396

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_4_deg	17.946
r_dihedral_angle_3_deg	16.049
r_lrange_it	8.083
r_lrange_other	8.055
r_dihedral_angle_1_deg	7.221
r_scangle_it	6.008
r_scangle_other	6.007
r_mcangle_it	4.736
r_mcangle_other	4.735
r_scbond_it	4.076
r_scbond_other	4.075
r_mcbond_other	3.252
r_mcbond_it	3.251
r_dihedral_angle_other_3_deg	1.836
r_angle_refined_deg	1.728
r_angle_other_deg	1.434
r_nbd_refined	0.205
r_symmetry_xyhbond_nbd_refined	0.198
r_xyhbond_nbd_refined	0.18
r_nbd_other	0.18
r_symmetry_nbd_other	0.177
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.147
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2341
Nucleic Acid Atoms
Solvent Atoms	177
Heterogen Atoms	47

Software

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