2GIB | pdb_00002gib

Crystal structure of the SARS coronavirus nucleocapsid protein dimerization domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277.5	30-33% Pentaerythritol ethoxylate 15/4 EO/OH, 50 mM Ammonium sulfate, 50 mM Bis-Tris , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.5K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.163	α = 90
b = 50.49	β = 108.92
c = 41.479	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	CCD	ADSC QUANTUM 315		2005-11-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97929, 0.97940, 0.94285	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.75	30.93	99.12			23293	23088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.75	1.795	96.12

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.75	30.93	23293	23088	1166	99.12	0.18951	0.18951	0.18726	0.21	0.23451	0.24	RANDOM	17.965

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]
-0.77		-0.47	-0.76		1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.36
r_dihedral_angle_3_deg	13.438
r_dihedral_angle_4_deg	11.965
r_sphericity_free	7.765
r_dihedral_angle_1_deg	6.036
r_scangle_it	3.912
r_scbond_it	3.124
r_sphericity_bonded	3.052
r_mcangle_it	2.177
r_rigid_bond_restr	2.142
r_angle_refined_deg	1.674
r_mcbond_it	1.627
r_symmetry_vdw_refined	0.538
r_symmetry_hbond_refined	0.419
r_nbtor_refined	0.313
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.223
r_chiral_restr	0.126
r_bond_refined_d	0.02
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1510
Nucleic Acid Atoms
Solvent Atoms	212
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
SOLVE	phasing