7Z0P | pdb_00007z0p

SARS-COV2 Main Protease in complex with inhibitor MG-131

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6Y2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9	293	0.1 M MMT, pH 9.0 plus 25% w/v polyethylenglycol 1500

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.716	α = 90
b = 51.667	β = 103.335
c = 45.451	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		2021-12-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.52	46.81	99	0.04	0.999	16.2	3.5		49867

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.52	2.62			0.996

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	6y2e	2.52	46.81	8752	420	98.781	0.208	0.2035	0.21	0.2898	0.29	44.003

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]
1.881		-1.283	0.932		-1.982

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.076
r_dihedral_angle_4_deg	22.426
r_dihedral_angle_3_deg	19.084
r_dihedral_angle_1_deg	9.324
r_lrange_it	7.922
r_lrange_other	7.921
r_dihedral_angle_other_3_deg	7.442
r_scangle_it	5.183
r_scangle_other	5.182
r_mcangle_it	4.981
r_mcangle_other	4.979
r_scbond_it	3.171
r_scbond_other	3.17
r_mcbond_other	3.151
r_mcbond_it	3.15
r_angle_refined_deg	1.592
r_angle_other_deg	1.185
r_symmetry_xyhbond_nbd_refined	0.256
r_chiral_restr	0.252
r_nbd_refined	0.225
r_nbd_other	0.221
r_symmetry_nbd_other	0.193
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.172
r_symmetry_nbd_refined	0.15
r_symmetry_nbtor_other	0.078
r_symmetry_xyhbond_nbd_other	0.033
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2347
Nucleic Acid Atoms
Solvent Atoms	37
Heterogen Atoms	41

Software

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