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Structure Aurora A (122-403) bound to activating monobody Mb1 and AMPPCP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4C3R PDB ENTRIES 4C3R AND 3K2M experimental model PDB 3K2M PDB ENTRIES 4C3R AND 3K2M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 AURORA A AND MONOBODIES WERE ALIQUOTED IN STORAGE BUFFER (20MM TRISHCL, 200MM NACL, 10% (V/V) GLYCEROL, 20MM MGCL2, 5MM TCEP, PH 7.50) AND KEPT AT -80C. AMPPCP WAS PREPARED FRESH FROM POWDER THE DAY OF CRYSTALLIZATION IN CONCENTRATIONS OF 100-120MM IN STORAGE BUFFER. CRYSTALS OF AURA IN COMPLEX WITH AMPPCP AND ACTIVATING MONOBODY, MB1, WERE OBTAINED BY COMBINING 0.5UL OF [300UM AURA WITH 5MM AMPPCP AND 300UM MB1] WITH 0.5UL OF MOTHER LIQUOR (0.1M MES SODIUM SALT PH 6.50, 0.2M AMMONIUM SULFATE, 4% (V/V) 1,3-PROPANEDIOL, 30% (W/V) PEG8000). CRYSTALS WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE SITTING DROP METHOD. THE CRYSTALS WERE WASHED WITH MOTHER LIQUOR AND FLASH FROZEN IN LIQUID NITROGEN IN PREPARATION FOR DATA COLLECTION.
Crystal Properties Matthews coefficient Solvent content 2.86 57.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.339 α = 90 b = 91.361 β = 90 c = 143.715 γ = 90
Symmetry Space Group I 2 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 CCD ADSC QUANTUM 315 2015-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 ALS 8.2.2
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 2.06 58.13 100 0.13 10.3 7.2 30879 1.8
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 2.06 2.12 99.5 1.21 1.8 7.2
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 PDB ENTRIES 4C3R AND 3K2M 2.06 77.1 29755 1052 99.71 0.22853 0.22687 0.2351 0.27388 0.2732 RANDOM 34.133
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] -0.02 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_4_deg 14.611 r_dihedral_angle_1_deg 7.235 r_mcangle_it 4.45 r_scbond_it 3.536 r_mcbond_it 2.914 r_mcbond_other 2.895 r_angle_refined_deg 1.916 r_angle_other_deg 1.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.402 r_dihedral_angle_3_deg 16.379 r_dihedral_angle_4_deg 14.611 r_dihedral_angle_1_deg 7.235 r_mcangle_it 4.45 r_scbond_it 3.536 r_mcbond_it 2.914 r_mcbond_other 2.895 r_angle_refined_deg 1.916 r_angle_other_deg 1.046 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it 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 2873 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 52
Software Software Software Name Purpose DIALS data reduction Aimless data scaling MOLREP phasing PHASER phasing REFMAC refinement