7QT5 | pdb_00007qt5

Room temperature In-situ SARS-CoV-2 MPRO with bound Z31792168

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	293	11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.773	α = 90
b = 54.595	β = 101.481
c = 45.313	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		2020-05-19	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	2.26	44.42	98.6	1.7	0.184	0.067	0.994	9.9	7		12834

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	2.26	2.34	99.6		1.956	2.11	0.767	0.425		7

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	7AEH	2.26	44.42	12833	646	98.564	0.171	0.1676	0.17	0.2313	0.23	48.917

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]
-0.795		-0.947	0.713		0.431

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.284
r_dihedral_angle_3_deg	17.725
r_dihedral_angle_4_deg	14.907
r_dihedral_angle_1_deg	8.351
r_lrange_other	5.197
r_lrange_it	5.166
r_scangle_it	3.408
r_scangle_other	3.407
r_mcangle_it	2.866
r_mcangle_other	2.865
r_scbond_it	2.174
r_scbond_other	2.173
r_mcbond_other	1.847
r_mcbond_it	1.846
r_angle_refined_deg	1.691
r_angle_other_deg	1.314
r_xyhbond_nbd_refined	0.205
r_nbd_refined	0.199
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.167
r_nbd_other	0.163
r_symmetry_nbd_refined	0.155
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_symmetry_xyhbond_nbd_other	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2325
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	20

Software

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