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Influenza C Virus RNA-dependent RNA Polymerase - Space group P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Drops were set up by mixing polymerase (5 mg/ml in 25 mM Hepes:NaOH, pH 7.5, 10% (v/v) glycerol, 0.5 M NaCl, 0.5 mM TCEP, 10 mM CaCl2) with 0.2 M NaCl, 0.1 M Na:HEPES, pH 7.5, 25% (w/v) PEG4000 and microseeds in a 2:1:1 protein:precipitant:seed ratio.
Crystal Properties Matthews coefficient Solvent content 3.42 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.28 α = 90 b = 217.5 β = 90 c = 597.75 γ = 90
Symmetry Space Group P 21 21 21
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 2014-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 4.3 80.9 99 0.204 5.5 3.3 95264
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.3 4.41 93.1 0.993 1.1 2.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5D98 4.3 50.01 90390 4744 98.8 0.31839 0.31575 0.3125 0.36847 0.3583 RANDOM 191.76
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] 4.39 3.98 -8.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.388 r_long_range_B_refined 27.76 r_long_range_B_other 27.759 r_mcangle_it 17.787 r_mcangle_other 17.787 r_dihedral_angle_3_deg 16.33 r_scangle_other 15.138 r_dihedral_angle_4_deg 10.574 r_mcbond_it 10.205 r_mcbond_other 10.205
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.388 r_long_range_B_refined 27.76 r_long_range_B_other 27.759 r_mcangle_it 17.787 r_mcangle_other 17.787 r_dihedral_angle_3_deg 16.33 r_scangle_other 15.138 r_dihedral_angle_4_deg 10.574 r_mcbond_it 10.205 r_mcbond_other 10.205 r_scbond_it 8.115 r_scbond_other 8.115 r_dihedral_angle_1_deg 6.303 r_angle_refined_deg 1.241 r_angle_other_deg 0.986 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 69371 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing