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Crystal structure of Nicotiana benthamiana importin alpha-Beet black scorch virus capsid protein NLS peptide complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OQS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.2 M lithium citrate, 35% glycerol
ethoxylate
Crystal Properties Matthews coefficient Solvent content 2.3 46.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.946 α = 90 b = 77.864 β = 89.88 c = 100.187 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 PIXEL DECTRIS PILATUS 2M 2012-01-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.9793 SSRF BL17U1
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 2.49 100.19 98.23 0.092 33.64 5.6 31906
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 2.49 2.576 0.092
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.49 100.19 31906 1709 98.23 0.18368 0.18135 0.1894 0.22573 0.2283 RANDOM 34.539
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] 0.23 -1.04 -4.66 4.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.817 r_dihedral_angle_4_deg 19.834 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 4.97 r_long_range_B_refined 4.51 r_long_range_B_other 4.508 r_scangle_other 2.632 r_mcangle_it 2.493 r_mcangle_other 2.493 r_scbond_it 1.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.817 r_dihedral_angle_4_deg 19.834 r_dihedral_angle_3_deg 16.751 r_dihedral_angle_1_deg 4.97 r_long_range_B_refined 4.51 r_long_range_B_other 4.508 r_scangle_other 2.632 r_mcangle_it 2.493 r_mcangle_other 2.493 r_scbond_it 1.513 r_scbond_other 1.513 r_mcbond_it 1.439 r_mcbond_other 1.435 r_angle_refined_deg 1.089 r_angle_other_deg 0.788 r_chiral_restr 0.06 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6713 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing