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Structural Basis for the Inhibition of Aurora A Kinase by a Novel Class of High Affinity Disubstituted Pyrimidine Inhibitors
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MQ4 pdb entry 1MQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 7% (w/v) PEG 400, 2.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.544 α = 90 b = 81.544 β = 90 c = 172.038 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 CCD NOIR-1 Si-monochromator 2006-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.24 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.25 70 99.4 0.076 0.076 8.6 4 16671 51
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.25 2.33 99.9 0.482 0.482 1.8 4 2001
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1MQ4 2.25 70.53 15822 15822 840 99.21 0.2457 0.2457 0.24421 0.2834 RANDOM 54.602
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] -1.06 -0.53 -1.06 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.75 r_dihedral_angle_4_deg 22.184 r_dihedral_angle_3_deg 16.707 r_dihedral_angle_1_deg 5.415 r_scangle_it 2.002 r_scbond_it 1.241 r_angle_refined_deg 1.149 r_mcangle_it 0.888 r_mcbond_it 0.498 r_symmetry_vdw_refined 0.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.75 r_dihedral_angle_4_deg 22.184 r_dihedral_angle_3_deg 16.707 r_dihedral_angle_1_deg 5.415 r_scangle_it 2.002 r_scbond_it 1.241 r_angle_refined_deg 1.149 r_mcangle_it 0.888 r_mcbond_it 0.498 r_symmetry_vdw_refined 0.421 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.195 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection d*TREK data reduction d*TREK data scaling PHASER phasing