7OA4

Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound L-742,001


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XI7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82933.4M Na-formate 0.1M Tris-HCl pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.8367.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 124.79α = 90
b = 124.79β = 90
c = 295.74γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-07-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 20.97563SOLEILPROXIMA 2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.9108.0711000.230.0430.99413.227.83115749.67
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)
12.92.9599.70.2020.9092.227.09

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-VALUE2XI72.9108.07131073154299.9810.1990.1970.238652.961
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]
0.3930.1970.393-1.276
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.228
r_dihedral_angle_3_deg15.762
r_dihedral_angle_4_deg13.343
r_dihedral_angle_1_deg5.768
r_lrange_it5.296
r_lrange_other5.294
r_scangle_it2.496
r_scangle_other2.496
r_mcangle_it2.237
r_mcangle_other2.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.228
r_dihedral_angle_3_deg15.762
r_dihedral_angle_4_deg13.343
r_dihedral_angle_1_deg5.768
r_lrange_it5.296
r_lrange_other5.294
r_scangle_it2.496
r_scangle_other2.496
r_mcangle_it2.237
r_mcangle_other2.237
r_scbond_it1.411
r_scbond_other1.411
r_mcbond_it1.302
r_mcbond_other1.302
r_angle_refined_deg1.211
r_angle_other_deg1.084
r_symmetry_xyhbond_nbd_refined0.221
r_nbd_refined0.183
r_nbtor_refined0.163
r_symmetry_nbd_other0.16
r_nbd_other0.159
r_xyhbond_nbd_refined0.158
r_symmetry_nbd_refined0.128
r_symmetry_nbtor_other0.072
r_symmetry_xyhbond_nbd_other0.062
r_chiral_restr0.046
r_bond_refined_d0.004
r_gen_planes_refined0.004
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 Atoms102
Heterogen Atoms142

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing