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Crystal structure of human Karyopherin-beta2 bound to the PY-NLS of Saccharomyces cerevisiae NAB2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QMR PDB entry 2QMR and 4FDD experimental model PDB 4FDD PDB entry 2QMR and 4FDD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 298 CRYSTALLIZATION CONDITIONS: PROTEIN (20 MM HEPES,
PH 7.3, 110 MM POTASSIUM ACETATE, 2MM MAGNESIUM ACETATE, 20% GLYCEROL, 2MM DTT);
RESERVOIR (MCSG3 #95: 0.7 M SODIUM CITRATE TRIBASIC, 100MM BIS-TRISPROPANTE pH
7.0); CRYOPROTECTION (20% GLYCEROL), temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 3.88 68.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.234 α = 90 b = 172.383 β = 90 c = 68.443 γ = 90
Symmetry Space Group P 21 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 315 MIRRORS 2011-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.07500 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 3.05 50 100 0.123 16.6 8.8 30914
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 3.05 3.1 100 1.18 9 1536
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2QMR and 4FDD 3.05 47.6 30636 1538 99.93 0.1867 0.1841 0.237 0.226 RANDOM 104.7336
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] -2.82 2.89 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.327 r_dihedral_angle_4_deg 23.163 r_dihedral_angle_3_deg 16.59 r_dihedral_angle_1_deg 6.582 r_angle_refined_deg 1.538 r_angle_other_deg 0.847 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.327 r_dihedral_angle_4_deg 23.163 r_dihedral_angle_3_deg 16.59 r_dihedral_angle_1_deg 6.582 r_angle_refined_deg 1.538 r_angle_other_deg 0.847 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6733 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-3000 data reduction SCALEPACK data scaling PHASER phasing