7QT7

Room temperature In-situ SARS-CoV-2 MPRO with bound Z4439011520

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	40.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.692	α = 90
b = 54.474	β = 101.698
c = 45.251	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	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)	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	2.25	44.35	95.2	0.162	0.174	0.061	0.987	8.9	7.2		12607

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	2.25	2.33			1.538	1.652	0.577	0.311	1.1

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	2.25	44.35	12604	618	95.146	0.165	0.1629	0.2163	47.168

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]
0.392		-0.345	0.252		-0.461

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.119
r_dihedral_angle_4_deg	16.042
r_dihedral_angle_3_deg	15.811
r_dihedral_angle_1_deg	7.883
r_dihedral_angle_other_2_deg	7.052
r_lrange_other	5.127
r_lrange_it	5.126
r_scangle_it	3.428
r_scangle_other	3.427
r_mcangle_it	2.668
r_mcangle_other	2.668
r_scbond_it	2.239
r_scbond_other	2.239
r_angle_refined_deg	1.81
r_mcbond_it	1.719
r_mcbond_other	1.716
r_angle_other_deg	1.34
r_symmetry_nbd_refined	0.289
r_chiral_restr	0.284
r_nbd_refined	0.209
r_nbd_other	0.203
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.173
r_xyhbond_nbd_refined	0.154
r_symmetry_nbtor_other	0.085
r_dihedral_angle_other_3_deg	0.032
r_bond_refined_d	0.011
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	2328
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	37

Software

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