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Crystal structure of RNA-binding domain of NS1 from influenza A virus A/crow/Kyoto/T1/2004(H5N1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AIL PDB ENTRY 1AIL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.8 293 0.1M SPG buffer pH 6.8, 25 % (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.89 34.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.723 α = 90 b = 54.378 β = 100.57 c = 66.347 γ = 90
Symmetry Space Group P 1 21 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 CCD RIGAKU JUPITER 210 rhodium coated mirror 2007-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000 SPring-8 BL26B2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.85 50 97.8 0.066 17.4 4 22185
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 90.9 0.274 2 3.4 2033
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB ENTRY 1AIL 1.85 50 -3 21044 1132 97.74 0.17584 0.17247 0.1781 0.23828 0.1776 RANDOM 17.504
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] 1.42 -0.57 -0.78 -0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.117 r_dihedral_angle_4_deg 18.684 r_dihedral_angle_3_deg 12.977 r_dihedral_angle_1_deg 3.564 r_scangle_it 1.965 r_scbond_it 1.261 r_angle_refined_deg 1 r_mcangle_it 0.672 r_mcbond_it 0.418 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.117 r_dihedral_angle_4_deg 18.684 r_dihedral_angle_3_deg 12.977 r_dihedral_angle_1_deg 3.564 r_scangle_it 1.965 r_scbond_it 1.261 r_angle_refined_deg 1 r_mcangle_it 0.672 r_mcbond_it 0.418 r_nbtor_refined 0.293 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.155 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2318 Nucleic Acid Atoms Solvent Atoms 286 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing