8BFO | pdb_00008bfo

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
2.02	39.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.98	α = 90
b = 53.933	β = 101.004
c = 44.738	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 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	1.98	48.71	98.6	0.987	7.75	4.83		18561

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	1.98	2.1	93.7		0.385	0.73	4.66

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	1.99	48.71	18512	900	99.473	0.216	0.212	0.22	0.2859	0.28	49.743

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]
0.822		-1.131	0.917		-1.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	24.882
r_dihedral_angle_3_deg	16.425
r_dihedral_angle_6_deg	16.307
r_lrange_it	8.494
r_lrange_other	8.484
r_dihedral_angle_1_deg	8.019
r_scangle_it	5.894
r_scangle_other	5.892
r_mcangle_other	5.428
r_mcangle_it	5.427
r_scbond_it	4.091
r_scbond_other	4.09
r_mcbond_it	4.005
r_mcbond_other	3.994
r_angle_refined_deg	1.324
r_angle_other_deg	0.733
r_nbd_other	0.235
r_symmetry_nbd_other	0.217
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.2
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.178
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.059
r_symmetry_xyhbond_nbd_other	0.021
r_gen_planes_other	0.009
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2358
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms

Software

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