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Crystal structure of Nicotiana benthamiana importin-alpha
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 0.1 M HEPES, pH 7.0, 0.1 M
ammonium formate , 20% Sokalan CP 7
Crystal Properties Matthews coefficient Solvent content 1.86 33.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.702 α = 93.05 b = 49.042 β = 105.62 c = 61.82 γ = 93.09
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 HEPS BPIX40-6M 2025-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON HEPS BEAMLINE ID02U1A 0.9793 HEPS ID02U1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.876 59.39 93.4 0.094 25.8 3.3 32273
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.876 1.925 0.094
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 1.88 59.39 30336 1620 91.96 0.217 0.21598 0.2288 0.23604 0.2491 RANDOM 38.698
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] 0.84 -3.2 1.97 -0.01 -3.8 -0.51
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.294 r_dihedral_angle_2_deg 38.697 r_sphericity_bonded 18.09 r_dihedral_angle_3_deg 17.053 r_dihedral_angle_4_deg 14.957 r_dihedral_angle_1_deg 4.515 r_rigid_bond_restr 1.706 r_angle_refined_deg 1.065 r_chiral_restr 0.08 r_bond_refined_d 0.006
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.294 r_dihedral_angle_2_deg 38.697 r_sphericity_bonded 18.09 r_dihedral_angle_3_deg 17.053 r_dihedral_angle_4_deg 14.957 r_dihedral_angle_1_deg 4.515 r_rigid_bond_restr 1.706 r_angle_refined_deg 1.065 r_chiral_restr 0.08 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3234 Nucleic Acid Atoms Solvent Atoms 379 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing