7EXM | pdb_00007exm

The N-terminal crystal structure of SARS-CoV-2 NSP2

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	PEG

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.926	α = 90
b = 159.603	β = 91.194
c = 63.552	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 2M		2020-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U	0.9793	SSRF	BL17U

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	1.96	50	93	0.999	17.9	6		89477

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	1.96	2.06			0.999

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	SAD	FREE R-VALUE	1.96	42.4	79154	4021	95.909	0.201	0.1997	0.21	0.2256	0.21	31.823

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]
0.057		0.053	-0.317		0.258

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.176
r_dihedral_angle_4_deg	15.558
r_dihedral_angle_3_deg	14.805
r_dihedral_angle_1_deg	6.403
r_lrange_it	4.495
r_lrange_other	4.434
r_mcangle_it	2.182
r_mcangle_other	2.182
r_scangle_it	2.152
r_scangle_other	2.152
r_angle_refined_deg	1.285
r_scbond_it	1.283
r_scbond_other	1.283
r_mcbond_it	1.262
r_mcbond_other	1.262
r_angle_other_deg	1.15
r_symmetry_nbd_other	0.171
r_nbd_other	0.17
r_nbd_refined	0.164
r_nbtor_refined	0.154
r_xyhbond_nbd_refined	0.135
r_symmetry_nbd_refined	0.129
r_symmetry_xyhbond_nbd_refined	0.115
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.045
r_symmetry_xyhbond_nbd_other	0.027
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8394
Nucleic Acid Atoms
Solvent Atoms	925
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL2Map	phasing