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Structural and mechanistical studies of the nuclear import by Importin-alpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 3%(v/v) Tacsimate pH5.0, 0.1M Sodium citrate tribasic dehydrate pH5.6, 16%(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.89 57.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.222 α = 90 b = 82.222 β = 90 c = 169.034 γ = 90
Symmetry Space Group P 41 21 2
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 ADSC QUANTUM 315r 2014-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 1.0050 SSRF BL17U
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 2.3 50 99.9 0.09 34 18.6 34657
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.37 100 5.7
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 3KND 2.3 47.9 25226 1301 99.81 0.21298 0.21144 0.2159 0.24253 0.2382 RANDOM 68.447
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] -0.01 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.497 r_dihedral_angle_4_deg 18.941 r_dihedral_angle_3_deg 18.079 r_long_range_B_other 13.197 r_long_range_B_refined 13.182 r_scangle_other 10.125 r_mcangle_it 9.049 r_mcangle_other 9.049 r_scbond_it 7.274 r_scbond_other 7.272
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.497 r_dihedral_angle_4_deg 18.941 r_dihedral_angle_3_deg 18.079 r_long_range_B_other 13.197 r_long_range_B_refined 13.182 r_scangle_other 10.125 r_mcangle_it 9.049 r_mcangle_other 9.049 r_scbond_it 7.274 r_scbond_other 7.272 r_mcbond_it 6.667 r_mcbond_other 6.664 r_dihedral_angle_1_deg 6.132 r_angle_refined_deg 1.805 r_angle_other_deg 1.038 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.002 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 3468 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing