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A transforming mutation in the pleckstrin homology domain of AKT1 in cancer (AKT1-PH_E17K)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UNQ PDB ENTRY 1UNQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 GROWN FROM HANGING DROPS IN 0.1 M HEPES PH 7.5 AND 1.4 M SODIUM CITRATE, OR 0.1 M ACETATE PH 4.6, 0.2 M AMMONIUM ACETATE AND 15%-30% PEG 3350,
Crystal Properties Matthews coefficient Solvent content 1.64 25.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.299 α = 90 b = 32.711 β = 116.67 c = 41.983 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC CCD MIRRORS 2006-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 2.46 37.5 97 0.08 13.5 2 3647 2
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 2.45 2.54 88.9 0.13 9.5 1.54
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1UNQ 2.46 37.53 3352 176 96.8 0.211 0.207 0.286 RANDOM 26.66
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] 1.23 0.15 -0.05 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.823 r_dihedral_angle_3_deg 21.337 r_dihedral_angle_4_deg 13.89 r_dihedral_angle_1_deg 7.051 r_scangle_it 2.302 r_angle_refined_deg 1.542 r_scbond_it 1.451 r_mcangle_it 1.341 r_mcbond_it 0.734 r_symmetry_hbond_refined 0.535
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.823 r_dihedral_angle_3_deg 21.337 r_dihedral_angle_4_deg 13.89 r_dihedral_angle_1_deg 7.051 r_scangle_it 2.302 r_angle_refined_deg 1.542 r_scbond_it 1.451 r_mcangle_it 1.341 r_mcbond_it 0.734 r_symmetry_hbond_refined 0.535 r_symmetry_vdw_refined 0.383 r_nbtor_refined 0.315 r_nbd_refined 0.25 r_xyhbond_nbd_refined 0.188 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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_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 985 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing