8HDA

Crystal structure of Ubl1 (residues 18-111) of SARS-CoV-2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7WZO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	15% w/v PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
1.73	25.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.53	α = 90
b = 46.333	β = 90
c = 70.077	γ = 90

Symmetry
Space Group	P 21 21 21

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		2020-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL19U1	0.9285	SSRF	BL19U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.93	19.81	99.3	0.094	0.041	0.995	10.7	6		11583

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.93	1.98	91.5		0.359	0.222	0.848	2.7	3.2

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7WZO	1.93	19.81	11544	602	99.116	0.186	0.1841	0.2287	34.064

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]
0.518			-0.861		0.342

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.785
r_dihedral_angle_4_deg	17.156
r_dihedral_angle_3_deg	13.143
r_lrange_other	7.563
r_lrange_it	7.561
r_dihedral_angle_1_deg	6.506
r_scangle_other	5.935
r_scangle_it	5.932
r_scbond_it	4.108
r_scbond_other	4.098
r_mcangle_it	3.885
r_mcangle_other	3.885
r_mcbond_it	2.819
r_mcbond_other	2.796
r_angle_refined_deg	1.536
r_angle_other_deg	1.343
r_symmetry_nbd_refined	0.262
r_symmetry_xyhbond_nbd_refined	0.228
r_nbd_other	0.222
r_xyhbond_nbd_refined	0.211
r_nbd_refined	0.2
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.167
r_ncsr_local_group_1	0.158
r_chiral_restr	0.081
r_symmetry_xyhbond_nbd_other	0.081
r_symmetry_nbtor_other	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1492
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
Aimless	data scaling
MOLREP	phasing