2GE8 | pdb_00002ge8

Structure of the C-terminal dimerization domain of infectious bronchitis virus nucleocapsid protein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GE7	PDB ENTRY 2GE7 4 copies

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.6	298	30% PEG 4000, 100 mM Tris-HCl pH 8.6, 800 mM LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 108.99	α = 90
b = 128.534	β = 90
c = 71.435	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	178	CCD	ADSC QUANTUM 4	Bent conical Si-mirror (Rh coated). Bent Ge(111) monochromator	2003-12-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.9000	APS	14-BM-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	2	129.473	95.8	0.115	0.115	4.8	4.4	69504	66258	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.11		97.3	0.013	0.01276	0.5	3.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2GE7 4 copies	2.2	47.78	2	69504	51179	2615	100	0.24	0.24	0.237	0.25	0.291	RANDOM	32.178

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]
-0.02			0.08		-0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.144
r_dihedral_angle_3_deg	19.133
r_dihedral_angle_4_deg	19.002
r_dihedral_angle_1_deg	8.373
r_scangle_it	4.531
r_scbond_it	2.906
r_angle_refined_deg	1.919
r_mcangle_it	1.719
r_mcbond_it	1.066
r_symmetry_hbond_refined	0.473

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.144
r_dihedral_angle_3_deg	19.133
r_dihedral_angle_4_deg	19.002
r_dihedral_angle_1_deg	8.373
r_scangle_it	4.531
r_scbond_it	2.906
r_angle_refined_deg	1.919
r_mcangle_it	1.719
r_mcbond_it	1.066
r_symmetry_hbond_refined	0.473
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.285
r_nbd_refined	0.251
r_xyhbond_nbd_refined	0.18
r_chiral_restr	0.142
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6881
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
CCP4	data scaling
PHASER	phasing
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.