7QT8 | pdb_00007qt8

Room temperature In-situ SARS-CoV-2 MPRO with bound ABT-957

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
2.1	41.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.245	α = 90
b = 54.673	β = 100.385
c = 116.578	γ = 90

Symmetry
Space Group	P 1 21 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		2020-07-02	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	2.01	49.37	95.2	0.17	0.184	0.067	0.994	9.9	7		37088

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	2.01	2.08	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	2.01	49.37	37088	1804	98.644	0.205	0.2037	0.21	0.2365	0.24	34.315

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]
1.078		-0.581	0.342		-1.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.302
r_dihedral_angle_4_deg	24.127
r_dihedral_angle_3_deg	15.924
r_dihedral_angle_other_3_deg	12.095
r_dihedral_angle_1_deg	7.866
r_lrange_it	3.507
r_lrange_other	3.502
r_scangle_it	2.283
r_scangle_other	2.282
r_angle_refined_deg	1.752
r_mcangle_it	1.639
r_mcangle_other	1.639
r_angle_other_deg	1.385
r_scbond_it	1.352
r_scbond_other	1.352
r_mcbond_it	0.967
r_mcbond_other	0.967
r_nbd_other	0.249
r_symmetry_nbd_refined	0.236
r_nbd_refined	0.207
r_symmetry_nbd_other	0.187
r_nbtor_refined	0.17
r_xyhbond_nbd_refined	0.128
r_chiral_restr	0.118
r_symmetry_xyhbond_nbd_refined	0.103
r_symmetry_nbtor_other	0.084
r_ncsr_local_group_1	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4695
Nucleic Acid Atoms
Solvent Atoms	48
Heterogen Atoms	72

Software

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