4FI5

Crystal structure of the N-terminal domain of Hantaan virus strain 76-118 nucleoprotein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IC9pdb ID 2ic9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5289HahaA.17785.a.A16.PS01490 at 20 mg/mL against Morpheus screen condition g8, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 20 mM Na-formate, 20 mM Na-citrate, 20 mM Ammonium acetate, 20 mM NaK tartrate, 100 mM MOPS/HEPES-Na pH 7.5, crystal tracking ID 234641g8, puck ID hky1-5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4650.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.4α = 90
b = 77.4β = 90
c = 36.52γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-05-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-11.003317SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.25099.80.07821.387.366196604-337.089
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.261000.5793.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb ID 2ic92.250659464599.760.19570.19150.2354RANDOM35.4455
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]
2.151.082.15-3.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.06
r_dihedral_angle_4_deg20.423
r_dihedral_angle_3_deg16.035
r_dihedral_angle_1_deg5.121
r_angle_refined_deg1.513
r_angle_other_deg0.951
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.06
r_dihedral_angle_4_deg20.423
r_dihedral_angle_3_deg16.035
r_dihedral_angle_1_deg5.121
r_angle_refined_deg1.513
r_angle_other_deg0.951
r_chiral_restr0.078
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms566
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction