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Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound L-742,001
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XI7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 3.4M Na-formate
0.1M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.83 67.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.79 α = 90 b = 124.79 β = 90 c = 295.74 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS EIGER X 16M 2020-07-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.97563 SOLEIL PROXIMA 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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.9 108.071 100 0.23 0.043 0.994 13.2 27.8 31157 49.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 2.95 99.7 0.202 0.909 2.2 27.09
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2XI7 2.9 108.071 31073 1542 99.981 0.199 0.197 0.2007 0.2386 0.2392 52.961
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] 0.393 0.197 0.393 -1.276
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.228 r_dihedral_angle_3_deg 15.762 r_dihedral_angle_4_deg 13.343 r_dihedral_angle_1_deg 5.768 r_lrange_it 5.296 r_lrange_other 5.294 r_scangle_it 2.496 r_scangle_other 2.496 r_mcangle_it 2.237 r_mcangle_other 2.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.228 r_dihedral_angle_3_deg 15.762 r_dihedral_angle_4_deg 13.343 r_dihedral_angle_1_deg 5.768 r_lrange_it 5.296 r_lrange_other 5.294 r_scangle_it 2.496 r_scangle_other 2.496 r_mcangle_it 2.237 r_mcangle_other 2.237 r_scbond_it 1.411 r_scbond_other 1.411 r_mcbond_it 1.302 r_mcbond_other 1.302 r_angle_refined_deg 1.211 r_angle_other_deg 1.084 r_symmetry_xyhbond_nbd_refined 0.221 r_nbd_refined 0.183 r_nbtor_refined 0.163 r_symmetry_nbd_other 0.16 r_nbd_other 0.159 r_xyhbond_nbd_refined 0.158 r_symmetry_nbd_refined 0.128 r_symmetry_nbtor_other 0.072 r_symmetry_xyhbond_nbd_other 0.062 r_chiral_restr 0.046 r_bond_refined_d 0.004 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 6132 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement xia2 data reduction DIALS data scaling PHASER phasing