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Crystal structure of the mouse Aurora-A catalytic domain (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with Compound 130.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3D14 PDB entry 3d14
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.9 293 Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 1.0 M sodium phosphate monobasic monohydrate, potassium phosphate dibasic pH 6.9; temperature: 293K; cryoprotectant: tacsimate; crystal frozen by immersion in liquid nitrogen.
Crystal Properties Matthews coefficient Solvent content 2.66 53.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.75 α = 90 b = 82.75 β = 90 c = 169.728 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 160 IMAGE PLATE RIGAKU RAXIS IV 2008-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54
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 2.8 30 99.2 0.051 19.3 7 9056 8957
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) 2.8 2.86 99.9 0.314 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 entry 3d14 2.8 22.83 8957 8016 888 98.48 0.26872 0.26571 0.2583 0.29553 0.2852 RANDOM 68.529
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] -1.68 -0.84 -1.68 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.56 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_4_deg 14.186 r_dihedral_angle_1_deg 4.583 r_mcangle_it 2.259 r_scangle_it 1.59 r_mcbond_it 1.31 r_angle_refined_deg 0.963 r_scbond_it 0.94 r_nbtor_refined 0.295
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.56 r_dihedral_angle_3_deg 15.132 r_dihedral_angle_4_deg 14.186 r_dihedral_angle_1_deg 4.583 r_mcangle_it 2.259 r_scangle_it 1.59 r_mcbond_it 1.31 r_angle_refined_deg 0.963 r_scbond_it 0.94 r_nbtor_refined 0.295 r_nbd_refined 0.166 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.105 r_symmetry_hbond_refined 0.083 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2065 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction d*TREK data scaling MOLREP phasing