7QT9

Room temperature In-situ SARS-CoV-2 MPRO with bound Z4439011584

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.5	298	11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.199	α = 90
b = 54.485	β = 101.092
c = 115.725	γ = 90

Symmetry
Space Group	I 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	298	PIXEL	DECTRIS PILATUS 6M-F		2020-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	1.0	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	2.43	56.846	97.9	0.166	0.183	0.073	0.987	10.8	5.9		10345

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	2.43	2.52	97.7		1.241	1.38	0.578	0.305		5.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7AEH	2.43	56.846	10339	543	97.87	0.152	0.1496	0.2003	45.722

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]
-0.609		0.211	-0.549		0.998

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35
r_dihedral_angle_3_deg	15.818
r_dihedral_angle_4_deg	14.355
r_dihedral_angle_other_2_deg	8.494
r_dihedral_angle_1_deg	8.161
r_lrange_it	5.563
r_lrange_other	5.562
r_scangle_it	4.01
r_scangle_other	4.009
r_mcangle_other	2.913
r_mcangle_it	2.912
r_scbond_it	2.483
r_scbond_other	2.482
r_angle_refined_deg	1.903
r_mcbond_it	1.831
r_mcbond_other	1.826
r_angle_other_deg	1.359
r_nbd_other	0.27
r_symmetry_nbd_refined	0.227
r_nbd_refined	0.211
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.162
r_symmetry_xyhbond_nbd_refined	0.117
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.076
r_dihedral_angle_other_3_deg	0.055
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
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	23
Heterogen Atoms	37

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
MOLREP	phasing