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Structure of Yeast Importin-beta (Kap95p)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BKU PDB ENTRY 2BKU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 20% PEG 4000, 0.1M MES pH 6.5, 20mM MgCl2, 125mM NaCl, 12% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.835 α = 90 b = 128.272 β = 102.68 c = 69.05 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 IMAGE PLATE RIGAKU RAXIS VII 2006-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54
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 2.4 30 0.075 11.4 37902
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2BKU 2.4 29.83 37902 35991 1901 97.06 0.21523 0.21254 0.201 0.26668 0.2518 RANDOM 54.93
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] -1.45 0.11 0.41 1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.526 r_dihedral_angle_3_deg 18.137 r_dihedral_angle_4_deg 17.706 r_dihedral_angle_1_deg 5.281 r_scangle_it 1.846 r_angle_refined_deg 1.243 r_scbond_it 1.146 r_mcangle_it 0.783 r_mcbond_it 0.431 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.526 r_dihedral_angle_3_deg 18.137 r_dihedral_angle_4_deg 17.706 r_dihedral_angle_1_deg 5.281 r_scangle_it 1.846 r_angle_refined_deg 1.243 r_scbond_it 1.146 r_mcangle_it 0.783 r_mcbond_it 0.431 r_nbtor_refined 0.292 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.084 r_bond_refined_d 0.012 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 6653 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling