6W6Y

Crystal Structure of ADP ribose phosphatase of NSP3 from SARS CoV-2 in complex with AMP

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6VXS	PDB entry 6VXS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	0.1 M MES, pH 6.5, 30% w/v PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.746	α = 90
b = 33.375	β = 95.086
c = 121.148	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 PILATUS3 X 6M		2020-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97918	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.45	50	98.6	0.109	0.99	21.3	5.3		52864

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.48	99.5		1.249	0.54		4.6

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	PDB entry 6VXS	1.451	40.256	52854	2627	98.264	0.144	0.1421	0.1891	25.777

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]
-0.322		0.737	-0.836		1.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.585
r_dihedral_angle_4_deg	22.141
r_dihedral_angle_3_deg	11.307
r_dihedral_angle_1_deg	6.6
r_scangle_it	5.723
r_scangle_other	5.721
r_rigid_bond_restr	4.39
r_mcangle_it	3.534
r_mcangle_other	3.534
r_mcbond_other	3.079
r_mcbond_it	3.052
r_angle_other_deg	1.689
r_angle_refined_deg	1.683
r_nbd_refined	0.217
r_symmetry_nbd_other	0.192
r_nbd_other	0.18
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.162
r_symmetry_nbd_refined	0.154
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.035
r_bond_other_d	0.014
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2535
Nucleic Acid Atoms
Solvent Atoms	299
Heterogen Atoms	35

Software

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