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Structure-based drug design of novel Aurora kinase A inhibitors: Structure basis for potency and specificity
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MQ4 PDB 1MQ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 22% PEG400, 0.1mM ammonia sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.51 51.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.613 α = 90 b = 81.613 β = 90 c = 169.145 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 ADSC QUANTUM 315 2007-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 NSRRC BL13B1
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 1.9 30 98 0.035 28.94 3.4 27121
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) 1.9 1.97 99.3 0.467 2.56 3.5
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 1MQ4 1.9 30 25207 1335 98.17 0.23055 0.22762 0.2332 0.28696 0.2872 RANDOM 39.695
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] -1.17 -0.59 -1.17 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.754 r_dihedral_angle_3_deg 18.344 r_dihedral_angle_4_deg 18.299 r_dihedral_angle_1_deg 6.132 r_scangle_it 3.785 r_scbond_it 2.257 r_mcangle_it 1.724 r_angle_refined_deg 1.413 r_mcbond_it 0.931 r_symmetry_hbond_refined 0.553
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.754 r_dihedral_angle_3_deg 18.344 r_dihedral_angle_4_deg 18.299 r_dihedral_angle_1_deg 6.132 r_scangle_it 3.785 r_scbond_it 2.257 r_mcangle_it 1.724 r_angle_refined_deg 1.413 r_mcbond_it 0.931 r_symmetry_hbond_refined 0.553 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.289 r_nbd_refined 0.245 r_xyhbond_nbd_refined 0.23 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2134 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling