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Crystal Structure of Nanobody PIK3_Nb16 against wild-type PI3Kalpha
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7R63
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.2 M Ammonium Sulfate, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.607 α = 90 b = 59.383 β = 111.06 c = 70.702 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 16M 2022-02-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.979338
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 1.85 29.75 97.5 0.086 0.105 0.059 0.996 7.8 2.9 39095
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 1.85 1.89 77.8 0.53 0.694 0.444 0.718 1.9
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 7R63 1.85 29.75 37195 1880 97.39 0.1922 0.18906 0.1982 0.25494 0.256 RANDOM 28
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] 1.61 1.1 -0.41 -1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_4_deg 17.565 r_dihedral_angle_3_deg 15.363 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 6.499 r_long_range_B_other 6.426 r_scangle_other 4.702 r_scbond_it 3.008 r_mcangle_it 2.987 r_mcangle_other 2.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.161 r_dihedral_angle_4_deg 17.565 r_dihedral_angle_3_deg 15.363 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 6.499 r_long_range_B_other 6.426 r_scangle_other 4.702 r_scbond_it 3.008 r_mcangle_it 2.987 r_mcangle_other 2.987 r_scbond_other 2.929 r_mcbond_it 2.044 r_mcbond_other 2.043 r_angle_refined_deg 1.473 r_angle_other_deg 1.325 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3805 Nucleic Acid Atoms Solvent Atoms 444 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction