2OFZ | pdb_00002ofz

Ultrahigh Resolution Crystal Structure of RNA Binding Domain of SARS Nucleopcapsid (N Protein) at 1.1 Angstrom Resolution in Monoclinic Form.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BTL	structure of homolog from infectious bronchitis virus PDB:2BTL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			25% PEG 2000MME, 0.2 M sodium bromide, 0.1 M sodium acetate, bcip ADDITIVE, VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.571	α = 90
b = 36.44	β = 94.71
c = 47.737	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	CCD	MARMOSAIC 325 mm CCD	mirrors	2005-05-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.9793	SSRL	BL11-1

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	1.17	47.57	97.4	0.062	0.059	22.19	3.8		40016			11.19

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)
	1.17	1.2	99.19		0.497	0.526	2.25	3.2	2882

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	structure of homolog from infectious bronchitis virus PDB:2BTL	1.17	47.57	40016	40016	2131	99.78	0.1638	0.16389	0.16244	0.21	0.19132	0.23	RANDOM	11.191

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]
0.16		0.05	0.3		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.657
r_dihedral_angle_4_deg	18.229
r_dihedral_angle_3_deg	12.61
r_dihedral_angle_1_deg	5.836
r_sphericity_free	5.087
r_scangle_it	3.208
r_sphericity_bonded	2.95
r_scbond_it	2.286
r_mcangle_it	1.77
r_angle_refined_deg	1.373
r_rigid_bond_restr	1.271
r_mcbond_it	1.166
r_symmetry_hbond_refined	0.479
r_symmetry_vdw_refined	0.324
r_nbtor_refined	0.304
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.172
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1100
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing