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Structure of full-length La Crosse virus L protein (polymerase)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AMR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 LACV-L in complex with pre-annealed 3 prime (1-16) and 5 prime (9-16) vRNA was concentrated to 5 mg/ml. The 5 prime (1-10) vRNA end was later soaked into crystals in 1 to 2 molar ratio. Mother liquor was 100 mM Tris pH 8.0, 100 mM NaCl, and 8% PEG 4000. Crystals were soaked in a stepwise manner with increasing concentration of the glycerol cryo-protectant, reaching 30%
Crystal Properties Matthews coefficient Solvent content 5.42 77.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 371.187 α = 90 b = 145.32 β = 116.333 c = 234.193 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M-F 2014-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9724 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 3.96 209.891 60.8 0.163 0.995 6.5 11.6 59211
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.96 4.35 1.285 0.47
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 5AMR 3.961 209.891 59211 1514 60.786 0.265 0.2638 0.2572 0.2988 0.29 189.756
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] 2.243 -1.674 1.232 -1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_3_deg 17.299 r_lrange_it 17.253 r_lrange_other 17.253 r_dihedral_angle_4_deg 11.115 r_mcangle_it 11.064 r_mcangle_other 11.064 r_scangle_it 8.98 r_scangle_other 8.98 r_mcbond_it 6.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.954 r_dihedral_angle_3_deg 17.299 r_lrange_it 17.253 r_lrange_other 17.253 r_dihedral_angle_4_deg 11.115 r_mcangle_it 11.064 r_mcangle_other 11.064 r_scangle_it 8.98 r_scangle_other 8.98 r_mcbond_it 6.307 r_mcbond_other 6.304 r_dihedral_angle_1_deg 5.017 r_scbond_it 4.781 r_scbond_other 4.781 r_angle_refined_deg 1.156 r_angle_other_deg 1.041 r_symmetry_xyhbond_nbd_refined 0.348 r_ext_dist_refined_d 0.222 r_nbd_other 0.182 r_symmetry_nbd_other 0.172 r_nbd_refined 0.17 r_nbtor_refined 0.159 r_xyhbond_nbd_refined 0.15 r_symmetry_nbd_refined 0.135 r_symmetry_nbtor_other 0.074 r_symmetry_xyhbond_nbd_other 0.066 r_ncsr_local_group_2 0.039 r_chiral_restr 0.038 r_ncsr_local_group_1 0.005 r_bond_refined_d 0.002 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 33204 Nucleic Acid Atoms 1434 Solvent Atoms Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling MOLREP phasing