5D9A

Influenza C Virus RNA-dependent RNA Polymerase - Space group P212121


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293Drops 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 coefficientSolvent content
3.4264

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.28α = 90
b = 217.5β = 90
c = 597.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
14.380.9990.2045.53.395264
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
14.34.4193.10.9931.12.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5D984.350.0190390474498.80.318390.315750.36847RANDOM191.76
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]
4.393.98-8.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.388
r_long_range_B_refined27.76
r_long_range_B_other27.759
r_mcangle_it17.787
r_mcangle_other17.787
r_dihedral_angle_3_deg16.33
r_scangle_other15.138
r_dihedral_angle_4_deg10.574
r_mcbond_it10.205
r_mcbond_other10.205
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.388
r_long_range_B_refined27.76
r_long_range_B_other27.759
r_mcangle_it17.787
r_mcangle_other17.787
r_dihedral_angle_3_deg16.33
r_scangle_other15.138
r_dihedral_angle_4_deg10.574
r_mcbond_it10.205
r_mcbond_other10.205
r_scbond_it8.115
r_scbond_other8.115
r_dihedral_angle_1_deg6.303
r_angle_refined_deg1.241
r_angle_other_deg0.986
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.003
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 AtomsNumber
Protein Atoms69371
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing