8BFQ | pdb_00008bfq

Structure of the apo form of Mpro from SARS-CoV-2

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	295	0.1 M sodium HEPES at pH 7.0 containing 22% PEG 4000 and 3% DMSO

Crystal Properties
Matthews coefficient	Solvent content
2	38.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.873	α = 90
b = 53.629	β = 100.827
c = 114.688	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	100	PIXEL	DECTRIS PILATUS 6M		2022-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97625	ALBA	XALOC

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	1.86	38.68	97.1	0.998	10.06	5.92		43744

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	1.86	1.98	92.5		0.595	1.08	5.64

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	7K3T	1.863	38.68	42906	2105	95.254	0.195	0.1922	0.2	0.2534	0.26	38.503

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]
0.689		0.194	-0.532		-0.215

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.16
r_dihedral_angle_3_deg	16.879
r_dihedral_angle_6_deg	15.761
r_lrange_it	8.757
r_lrange_other	8.754
r_dihedral_angle_1_deg	7.694
r_scangle_it	6.787
r_scangle_other	6.786
r_mcangle_other	4.848
r_mcangle_it	4.847
r_scbond_it	4.734
r_scbond_other	4.731
r_mcbond_it	3.616
r_mcbond_other	3.612
r_angle_refined_deg	1.582
r_angle_other_deg	0.862
r_symmetry_xyhbond_nbd_other	0.414
r_nbd_other	0.231
r_symmetry_nbd_refined	0.229
r_nbd_refined	0.227
r_symmetry_nbd_other	0.226
r_xyhbond_nbd_refined	0.219
r_nbtor_refined	0.187
r_symmetry_xyhbond_nbd_refined	0.17
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.073
r_gen_planes_other	0.011
r_bond_refined_d	0.009
r_gen_planes_refined	0.009
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4736
Nucleic Acid Atoms
Solvent Atoms	258
Heterogen Atoms

Software

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