9QD5 | pdb_00009qd5

Crystal structure of SARS-CoV-2 main protease in complex with RS222C

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6LU7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.7	293	100 mM MES pH 6.7, 11% PEG 4000 and 5% DMSO 150 nL Protein (5 mg/mL), 150 nL Crystallisation condition, 50 nL seed stock (1:250)

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.742	α = 90
b = 99.931	β = 90
c = 104.108	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER2 XE 16M		2023-07-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	2.044	72.093	93.2	0.1988	0.2068	0.0561	0.918	9.71	13.21		31215

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)
	2.044	2.23	60.4		1.8226	1.8917	0.5023	0.665	1.61	13.36	1561

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	2.044	72.093	31215	1594	68.674	0.192	0.1902	0.1986	0.2319	0.2368	35.256

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]
0.301			-0.738		0.437

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	21.45
r_dihedral_angle_6_deg	14.356
r_dihedral_angle_3_deg	13.717
r_lrange_it	9.453
r_lrange_other	9.443
r_scangle_it	7.919
r_scangle_other	7.918
r_dihedral_angle_1_deg	6.38
r_scbond_it	5.677
r_scbond_other	5.675
r_mcangle_other	4.992
r_mcangle_it	4.988
r_mcbond_it	3.602
r_mcbond_other	3.589
r_angle_refined_deg	1.377
r_angle_other_deg	0.418
r_symmetry_nbd_refined	0.262
r_nbd_other	0.239
r_symmetry_xyhbond_nbd_other	0.215
r_symmetry_nbd_other	0.208
r_nbd_refined	0.207
r_metal_ion_refined	0.2
r_nbtor_refined	0.177
r_xyhbond_nbd_refined	0.167
r_symmetry_xyhbond_nbd_refined	0.143
r_ncsr_local_group_1	0.096
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.068
r_bond_refined_d	0.01
r_gen_planes_other	0.006
r_gen_planes_refined	0.004
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4604
Nucleic Acid Atoms
Solvent Atoms	281
Heterogen Atoms	41

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
REFMAC	refinement