8AJ1 | pdb_00008aj1

SARS-CoV-2 Mpro in Complex with RK-107

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	7	293	0.1M PCTP pH7.0, 25% w/vPEG 1500

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.234	α = 90
b = 52.955	β = 102.806
c = 45.707	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		2021-12-06	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)	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	2.6	47.793	98	0.996	7.1	3.5		8125

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	2.6	2.69	98		0.508

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.6	47.793	8124	397	98.246	0.2	0.1953	0.2036	0.2745	0.2831	69.138

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]
6.333		1.274	0.377		-6.607

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.032
r_dihedral_angle_3_deg	17.702
r_dihedral_angle_6_deg	13.969
r_lrange_it	10.82
r_lrange_other	10.819
r_scangle_it	7.555
r_scangle_other	7.553
r_dihedral_angle_1_deg	7.44
r_mcangle_it	6.769
r_mcangle_other	6.768
r_scbond_it	4.728
r_scbond_other	4.727
r_mcbond_it	4.435
r_mcbond_other	4.431
r_dihedral_angle_other_3_deg	3.205
r_angle_refined_deg	1.122
r_angle_other_deg	0.381
r_nbd_refined	0.224
r_symmetry_nbd_other	0.205
r_nbd_other	0.196
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_refined	0.178
r_xyhbond_nbd_refined	0.15
r_symmetry_nbd_refined	0.127
r_symmetry_nbtor_other	0.082
r_xyhbond_nbd_other	0.066
r_symmetry_xyhbond_nbd_other	0.063
r_chiral_restr	0.049
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
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	22
Heterogen Atoms	39

Software

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