9HDC

SARS-CoV-2 Main Protease in complex with (3S)-3-[(3R)-3-phenylpiperidine-1-carbonyl]indan-1-one

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7K3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.5	293	0.2 M sodium formate, 20% PEG 3350. Then soaking with inhibitor (DMSO) and cryo-protection with glycerol (10%).

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.64	α = 90
b = 53.58	β = 102.72
c = 44.83	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 9M		2022-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.9184	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.794	48.367	99.3	0.076	0.082	0.999	13.3	6.8		24802			31.62

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.794	1.84	93.6		1.036	1.126	0.626	1.5

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.794	48.367	24801	1240	99.403	0.172	0.1693	0.2287	35.277

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]
1.362		0.779	-1.296		-0.379

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.408
r_dihedral_angle_2_deg	13.445
r_dihedral_angle_3_deg	12.842
r_lrange_it	7.67
r_lrange_other	7.655
r_dihedral_angle_1_deg	7.593
r_scangle_it	6.716
r_scangle_other	6.715
r_scbond_it	4.814
r_scbond_other	4.802
r_mcangle_it	3.832
r_mcangle_other	3.831
r_mcbond_other	2.965
r_mcbond_it	2.963
r_angle_refined_deg	2.427
r_angle_other_deg	0.852
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.215
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.195
r_nbtor_refined	0.192
r_symmetry_xyhbond_nbd_refined	0.172
r_nbd_other	0.154
r_chiral_restr	0.138
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_other	0.018
r_bond_refined_d	0.016
r_gen_planes_refined	0.015
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2348
Nucleic Acid Atoms
Solvent Atoms	137
Heterogen Atoms	35

Software

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