8F02 | pdb_00008f02

SARS-CoV-2 Main Protease (Mpro) in Complex with ML2006a4

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	Sitting drops consisted of 0.23 uL A:0.23 uL B: A) 5.3 mg/mL Mpro + 0.9 mM ML2006a4 in in 20 mM Tris pH 7.3 + 3 mM TCEP + 3 % DMSO B) 0.1 M BICINE pH 8.5, 8% w/v mPEG 5000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.649	α = 90
b = 63.231	β = 90
c = 103.798	γ = 90

Symmetry
Space Group	P 21 21 2

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	Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2	2022-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	37.04	97.9	0.123	0.057	0.997	5.5	4.3		20441

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.11		99.6	2.19	1.021	0.255		4.3

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6LZE	2	37.04	19391	1032	97.28	0.19297	0.18974	0.2	0.25476	0.26	RANDOM	51.68

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]
-0.81			1.94		-1.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.311
r_long_range_B_other	9.513
r_long_range_B_refined	9.511
r_dihedral_angle_2_deg	9.334
r_dihedral_angle_1_deg	7.827
r_scangle_other	7.369
r_mcangle_other	5.741
r_mcangle_it	5.74
r_scbond_it	4.94
r_scbond_other	4.937
r_mcbond_it	4.035
r_mcbond_other	4.013
r_angle_refined_deg	1.52
r_angle_other_deg	0.492
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2367
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	44

Software

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