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Crystal structure of the full-length simian virus 40 small t antigen complexed with the protein phosphatase 2A Aalpha subunit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IAE PDB ENTRY 2IAE-A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 298 16% PEG 3350,
0.2 M Ammonium formate,
30 mM spermine,
6% 6-aminocaproic acid,
10 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 8.00
Crystal Properties Matthews coefficient Solvent content 2.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.711 α = 115.64 b = 105.501 β = 109.55 c = 111.937 γ = 94.11
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 210 2007-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 3.1 50 98 0.076 0.076 12.1 7.1 62693 1.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.21 88.7 0.758 0.758 1.8 4.8
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2IAE-A 3.1 20 59306 3159 97.4 0.247 0.244 0.2367 0.304 RANDOM 114.44
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] 3.04 -0.5 1.94 -2.8 -1.19 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.301 r_dihedral_angle_3_deg 20.662 r_dihedral_angle_4_deg 19.111 r_dihedral_angle_1_deg 5.855 r_scangle_it 1.563 r_angle_refined_deg 1.387 r_scbond_it 0.933 r_mcangle_it 0.704 r_mcbond_it 0.391 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.301 r_dihedral_angle_3_deg 20.662 r_dihedral_angle_4_deg 19.111 r_dihedral_angle_1_deg 5.855 r_scangle_it 1.563 r_angle_refined_deg 1.387 r_scbond_it 0.933 r_mcangle_it 0.704 r_mcbond_it 0.391 r_nbtor_refined 0.303 r_nbd_refined 0.243 r_symmetry_vdw_refined 0.238 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.091 r_symmetry_hbond_refined 0.08 r_metal_ion_refined 0.018 r_bond_refined_d 0.009 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_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 22794 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing SHARP phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling