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Crystal Structure of PI5P4KIIAlpha complex with 066ATZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YBX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.2 M Lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 25% (w/v) Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.96 58.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.493 α = 90 b = 136.493 β = 90 c = 94.904 γ = 120
Symmetry Space Group P 61 2 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 PIXEL DECTRIS EIGER X 9M 2023-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.97934 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) 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 2.4 40 99.9 0.064 0.068 0.02 12.8 10.8 20802 79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 0.295 0.911
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.404 39.433 20770 971 99.798 0.187 0.1838 0.1824 0.2429 0.2412 78.782
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] 1.6 0.8 1.6 -5.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.812 r_dihedral_angle_6_deg 15.558 r_lrange_it 15.416 r_scangle_it 11.488 r_mcangle_it 9.977 r_scbond_it 7.858 r_dihedral_angle_1_deg 7.229 r_mcbond_it 6.663 r_dihedral_angle_2_deg 5.559 r_angle_refined_deg 1.281
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.812 r_dihedral_angle_6_deg 15.558 r_lrange_it 15.416 r_scangle_it 11.488 r_mcangle_it 9.977 r_scbond_it 7.858 r_dihedral_angle_1_deg 7.229 r_mcbond_it 6.663 r_dihedral_angle_2_deg 5.559 r_angle_refined_deg 1.281 r_nbtor_refined 0.31 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.188 r_symmetry_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.127 r_chiral_restr 0.094 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2490 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing