33VD | pdb_000033vd

SAD-phased structure of SARS-CoV-2 Nucleocapsid protein CTD.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.8	293	0.1 M HEPES, pH 7.8 10 % isopropanol 23% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.12	42.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.5	α = 90
b = 88.5	β = 90
c = 39.4	γ = 90

Symmetry
Space Group	P 43

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 12M		2026-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	1.9074	Diamond	I23

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	1.23	44.25	92.78	1	22.4	6.7		82406

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	1.23	1.25			0.973

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	FREE R-VALUE	1.23	44.25	82385	4157	92.757	0.149	0.1478	0.148	0.1741	0.1749	RANDOM	17.725

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]
1.023			1.023		-2.047

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.44
r_dihedral_angle_6_deg	15.266
r_lrange_other	13.561
r_dihedral_angle_2_deg	13.378
r_dihedral_angle_3_deg	10.144
r_scangle_it	8.604
r_scangle_other	8.603
r_dihedral_angle_1_deg	7.022
r_mcangle_other	6.501
r_mcangle_it	6.496
r_scbond_other	6.322
r_scbond_it	6.321
r_mcbond_it	4.798
r_mcbond_other	4.786
r_rigid_bond_restr	4.352
r_angle_refined_deg	1.977
r_angle_other_deg	1.015
r_nbd_refined	0.215
r_nbtor_refined	0.163
r_symmetry_nbd_other	0.147
r_nbd_other	0.139
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.113
r_symmetry_nbd_refined	0.111
r_symmetry_xyhbond_nbd_refined	0.109
r_ncsr_local_group_1	0.1
r_symmetry_nbtor_other	0.065
r_gen_planes_refined	0.015
r_bond_refined_d	0.012
r_gen_planes_other	0.006
r_bond_other_d	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2525
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	40

Software

Software
Software Name	Purpose
Aimless	data scaling
XDS	data reduction
gemmi	data extraction
REFMAC	refinement
CRANK2	phasing