5H43

Structural and mechanistical studies of the nuclear import by Importin-alpha


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3KND 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.153%(v/v) Tacsimate pH5.0, 0.1M Sodium citrate tribasic dehydrate pH5.6, 16%(w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8957.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.222α = 90
b = 82.222β = 90
c = 169.034γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U1.0050SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35099.90.093418.634657
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.312.371005.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3KND2.347.925226130199.810.212980.211440.24253RANDOM68.447
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.497
r_dihedral_angle_4_deg18.941
r_dihedral_angle_3_deg18.079
r_long_range_B_other13.197
r_long_range_B_refined13.182
r_scangle_other10.125
r_mcangle_it9.049
r_mcangle_other9.049
r_scbond_it7.274
r_scbond_other7.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.497
r_dihedral_angle_4_deg18.941
r_dihedral_angle_3_deg18.079
r_long_range_B_other13.197
r_long_range_B_refined13.182
r_scangle_other10.125
r_mcangle_it9.049
r_mcangle_other9.049
r_scbond_it7.274
r_scbond_other7.272
r_mcbond_it6.667
r_mcbond_other6.664
r_dihedral_angle_1_deg6.132
r_angle_refined_deg1.805
r_angle_other_deg1.038
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms3468
Nucleic Acid Atoms
Solvent Atoms146
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing