3FDN

Structure-based drug design of novel Aurora kinase A inhibitors: Structure basis for potency and specificity


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MQ4PDB 1MQ4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529122% PEG400, 0.1mM ammonia sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.5151.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.613α = 90
b = 81.613β = 90
c = 169.145γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B1NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.930980.03528.943.427121
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.91.9799.30.4672.563.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB 1MQ41.93025207133598.170.230550.227620.28696RANDOM39.695
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]
-1.17-0.59-1.171.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.754
r_dihedral_angle_3_deg18.344
r_dihedral_angle_4_deg18.299
r_dihedral_angle_1_deg6.132
r_scangle_it3.785
r_scbond_it2.257
r_mcangle_it1.724
r_angle_refined_deg1.413
r_mcbond_it0.931
r_symmetry_hbond_refined0.553
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.754
r_dihedral_angle_3_deg18.344
r_dihedral_angle_4_deg18.299
r_dihedral_angle_1_deg6.132
r_scangle_it3.785
r_scbond_it2.257
r_mcangle_it1.724
r_angle_refined_deg1.413
r_mcbond_it0.931
r_symmetry_hbond_refined0.553
r_nbtor_refined0.312
r_symmetry_vdw_refined0.289
r_nbd_refined0.245
r_xyhbond_nbd_refined0.23
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2134
Nucleic Acid Atoms
Solvent Atoms199
Heterogen Atoms30

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling