5E2X

The crystal structure of the C-terminal domain of Ebola (Tai Forest) nucleoprotein

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4QB0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.64	293	Crystallization conditions: 10% PEG 3350, 0.1 M Tris-HCl/HEPES pH 8.64. 1:1 ratio of precipitant solution to protein, with a protein concentration of 5.0 mg/mL. There was a 1.5 M NaCl alternative reservoir

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.847	α = 69.15
b = 60.075	β = 68.93
c = 73.547	γ = 89.93

Symmetry
Space Group	P 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 315r		2014-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.979	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.1	50	96.1	0.07	0.096	0.065	7.8	2.1		48426

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	84.6		0.316	0.436	0.299	0.789		2	2124

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4QB0	2.1	50	45777	2235	96.2	0.1946	0.1914	0.2597	RANDOM	41.867

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]
-2.73	0.17	-0.64	-1.22	-0.83	1.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.132
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_4_deg	10.349
r_mcangle_it	5.328
r_dihedral_angle_1_deg	5.271
r_mcbond_it	4.279
r_mcbond_other	4.275
r_angle_refined_deg	1.092
r_angle_other_deg	0.894
r_chiral_restr	0.064

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.132
r_dihedral_angle_3_deg	13.126
r_dihedral_angle_4_deg	10.349
r_mcangle_it	5.328
r_dihedral_angle_1_deg	5.271
r_mcbond_it	4.279
r_mcbond_other	4.275
r_angle_refined_deg	1.092
r_angle_other_deg	0.894
r_chiral_restr	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6732
Nucleic Acid Atoms
Solvent Atoms	664
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
SCALEPACK	data scaling
HKL-3000	data reduction
MOLREP	phasing
Coot	model building
PDB_EXTRACT	data extraction

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 R01GM133198.