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Crystal structure of smAKAP AKB domain bound RIa dimerization/docking (D/D) complex at 2.0 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 3.5 297 a 2:3 ratio of protein solution:crystallizing (crystallizing solution: 0.1 M Citric acid pH 3.5, 28% w/v Polyethylene glycol 8,000)
Crystal Properties Matthews coefficient Solvent content 2.02 39.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.511 α = 90 b = 55.737 β = 90 c = 57.268 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 200 CCD ADSC QUANTUM 315 2012-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
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 2 50 98 0.076 0.061 26.9 5.2 8480
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.46 4 5.4
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 3IM4 2 39.94 7937 392 97.53 0.21127 0.20976 0.2043 0.24133 0.2226 RANDOM 30.44
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] -0.43 0.65 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.184 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 18.682 r_scangle_it 7.258 r_dihedral_angle_1_deg 5.439 r_scbond_it 4.345 r_mcangle_it 2.656 r_angle_refined_deg 1.891 r_mcbond_it 1.437 r_chiral_restr 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.184 r_dihedral_angle_4_deg 23.253 r_dihedral_angle_3_deg 18.682 r_scangle_it 7.258 r_dihedral_angle_1_deg 5.439 r_scbond_it 4.345 r_mcangle_it 2.656 r_angle_refined_deg 1.891 r_mcbond_it 1.437 r_chiral_restr 0.151 r_bond_other_d 0.024 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 959 Nucleic Acid Atoms Solvent Atoms 29 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing