7PLR

Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound Baloxavir


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7OA4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82933.4M Sodium Formate 0.1M Tris - HCl pH8.0
Crystal Properties
Matthews coefficientSolvent content
3.8267.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.738α = 90
b = 124.738β = 90
c = 295.25γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.97856SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
12.64108.031000.0250.99920.139.840890
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.642.691000.190.9122.239.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE7OA42.64108.0264079920411000.2160.21360.253955.557
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]
0.8110.4060.811-2.632
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.307
r_dihedral_angle_3_deg14.438
r_dihedral_angle_4_deg12.758
r_dihedral_angle_1_deg5.503
r_lrange_it4.608
r_lrange_other4.598
r_scangle_it2.853
r_scangle_other2.853
r_mcangle_it2.687
r_mcangle_other2.686
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.307
r_dihedral_angle_3_deg14.438
r_dihedral_angle_4_deg12.758
r_dihedral_angle_1_deg5.503
r_lrange_it4.608
r_lrange_other4.598
r_scangle_it2.853
r_scangle_other2.853
r_mcangle_it2.687
r_mcangle_other2.686
r_scbond_it1.72
r_scbond_other1.718
r_mcbond_it1.648
r_mcbond_other1.648
r_angle_refined_deg1.204
r_angle_other_deg1.089
r_symmetry_xyhbond_nbd_refined0.275
r_nbd_refined0.185
r_nbtor_refined0.162
r_symmetry_nbd_other0.158
r_xyhbond_nbd_refined0.145
r_symmetry_nbd_refined0.138
r_nbd_other0.126
r_symmetry_nbtor_other0.07
r_xyhbond_nbd_other0.056
r_chiral_restr0.045
r_gen_planes_refined0.004
r_bond_refined_d0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6132
Nucleic Acid Atoms
Solvent Atoms63
Heterogen Atoms130

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing