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Crystal structure of Aurora-A bound to DBS4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.09M NPS, 0.1M Buffer system 2 pH 7.5, 30% Precipitant mix 1
Crystal Properties Matthews coefficient Solvent content 2.89 57.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.33 α = 90 b = 88.33 β = 90 c = 240.29 γ = 90
Symmetry Space Group P 41 21 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 EIGER2 X 16M 2024-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.23 60.45 99.9 1 14.1 26.4 47348
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.23 2.27 0.6
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 FREE R-VALUE 2.23 60.45 47251 2318 99.698 0.204 0.2014 0.2087 0.2493 0.2549 62.602
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] -0.349 -0.349 0.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.387 r_dihedral_angle_3_deg 12.757 r_lrange_other 11.255 r_lrange_it 11.25 r_dihedral_angle_2_deg 9.461 r_scangle_it 8.913 r_scangle_other 8.887 r_mcangle_it 7.279 r_mcangle_other 7.278 r_dihedral_angle_1_deg 6.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.387 r_dihedral_angle_3_deg 12.757 r_lrange_other 11.255 r_lrange_it 11.25 r_dihedral_angle_2_deg 9.461 r_scangle_it 8.913 r_scangle_other 8.887 r_mcangle_it 7.279 r_mcangle_other 7.278 r_dihedral_angle_1_deg 6.226 r_scbond_it 6.181 r_scbond_other 6.169 r_mcbond_it 5.246 r_mcbond_other 5.239 r_angle_refined_deg 1.306 r_angle_other_deg 0.469 r_nbd_refined 0.216 r_symmetry_nbd_other 0.187 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.178 r_symmetry_nbd_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.167 r_nbd_other 0.153 r_metal_ion_refined 0.101 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_2 0.08 r_chiral_restr 0.066 r_dihedral_angle_other_2_deg 0.02 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5039 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing