3HHW | pdb_00003hhw

Complex of a vesicular stomatitis virus empty capsid with the nucleocapsid-binding domain of the phosphoprotein

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	295	0.8 M K/Na tartrate, 0.2 M NaCl, 0.1 M imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 170.602	α = 90
b = 234.52	β = 90
c = 95.05	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	100	CCD	MARMOSAIC 300 mm CCD		2008-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	0.94	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.7	30	73.1	0.073	20.79		77814	77814

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.8	44.9		0.419

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	PDB ENTRY 2QVJ	2.7	30	73762	73762	3840	73.67	0.26447	0.26447	0.26286	0.26	0.29573	0.3	RANDOM	74.58

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]
3.36			-0.23		-3.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.89
r_dihedral_angle_3_deg	17.028
r_dihedral_angle_4_deg	13.875
r_dihedral_angle_1_deg	4.387
r_angle_refined_deg	0.957
r_scangle_it	0.696
r_mcangle_it	0.554
r_scbond_it	0.409
r_mcbond_it	0.305
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.89
r_dihedral_angle_3_deg	17.028
r_dihedral_angle_4_deg	13.875
r_dihedral_angle_1_deg	4.387
r_angle_refined_deg	0.957
r_scangle_it	0.696
r_mcangle_it	0.554
r_scbond_it	0.409
r_mcbond_it	0.305
r_nbtor_refined	0.297
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.121
r_xyhbond_nbd_refined	0.104
r_symmetry_hbond_refined	0.078
r_chiral_restr	0.067
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19555
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	60

Software

Software
Software Name	Purpose
SERGUI	data collection
COMO	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

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.