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Crystal structure of Akt1 (aa 123-480) kinase with a bisubstrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BUU PDB entry 6BUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 277 12.5% PEG3350, 0.1 M HEPES-HCl, 0.2 M ammonium acetate
Crystal Properties Matthews coefficient Solvent content 2.5 50.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.321 α = 90 b = 56.088 β = 104.56 c = 92.019 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 9M 2017-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.99958 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.12 29.82 98.5 0.11 0.119 0.046 0.996 10.2 6.8 48316
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.18 83.5 0.721 0.782 0.297 0.838 6.6
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 6BUU 2.12 29.82 45932 2364 99.03 0.1881 0.1853 0.1984 0.241 0.2417 RANDOM 39.787
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] -0.15 1.28 -0.72 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.454 r_dihedral_angle_4_deg 19.924 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 2.06 r_angle_other_deg 1.517 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.454 r_dihedral_angle_4_deg 19.924 r_dihedral_angle_3_deg 16.329 r_dihedral_angle_1_deg 7.045 r_angle_refined_deg 2.06 r_angle_other_deg 1.517 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.013 r_gen_planes_other 0.009 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5514 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 35
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing