3DJ5

Crystal structure of the mouse Aurora-A catalytic domain (Asn186->Gly, Lys240->Arg, Met302->Leu) in complex with Compound 290.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C6DPDB entry 2c6d

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.6293Protein at 8.5 mg/ml in 50 mM Tris pH 7.0, 200 mM NaCl, 3 mM DTT; hanging-drop vapor diffusion; mother liquor: 0.1 M sodium citrate tribasic dihydrate pH 5.6, 2% tacsimate, 16% PEG 3350; temperature: 293K; cryoprotectant: 20% glycerol; crystal frozen by immersion in liquid nitrogen
Crystal Properties
Matthews coefficientSolvent content
2.7254.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.738α = 90
b = 97.738β = 90
c = 62.224γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray160CCDADSC QUANTUM 315Vertical focusing mirror2008-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.98SSRLBL7-1

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
11.83098.70.05316.63.83209831664
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)
1.81.8699.80.1674.9

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 entry 2c6d1.83029178244998.560.20990.207150.24299RANDOM26.476
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]
0.50.250.5-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.545
r_dihedral_angle_4_deg21.574
r_dihedral_angle_3_deg15.266
r_dihedral_angle_1_deg5.152
r_scangle_it4.906
r_mcangle_it3.682
r_scbond_it3.465
r_mcbond_it2.642
r_angle_refined_deg1.166
r_nbtor_refined0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.545
r_dihedral_angle_4_deg21.574
r_dihedral_angle_3_deg15.266
r_dihedral_angle_1_deg5.152
r_scangle_it4.906
r_mcangle_it3.682
r_scbond_it3.465
r_mcbond_it2.642
r_angle_refined_deg1.166
r_nbtor_refined0.3
r_nbd_refined0.197
r_symmetry_vdw_refined0.185
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.142
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.003
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 AtomsNumber
Protein Atoms2077
Nucleic Acid Atoms
Solvent Atoms369
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
CrystalCleardata reduction
d*TREKdata scaling
MOLREPphasing