3E5A

Crystal structure of Aurora A in complex with VX-680 and TPX2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OL5PDB entry 1OL5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.929316% PEG 3350 and 0.2 M Lithium sulfate buffered with 100 mM Bis-Tris, pH 6.9, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
2.2846.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.186α = 90
b = 89.097β = 90
c = 88.499γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.0000APS17-ID

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.35097.10.0720.06225.65.615823153652
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)RedundancyNumber Unique Reflections (All)
12.32.3878.20.4090.2722.74.61215

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 1OL52.3251281483387.320.206280.203180.25585RANDOM52.914
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]
4.61-4.1-0.51
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.281
r_dihedral_angle_4_deg18.967
r_dihedral_angle_3_deg15.504
r_dihedral_angle_1_deg7.756
r_scangle_it3.381
r_scbond_it2.15
r_angle_refined_deg1.659
r_mcangle_it1.239
r_mcbond_it0.742
r_symmetry_hbond_refined0.348
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.281
r_dihedral_angle_4_deg18.967
r_dihedral_angle_3_deg15.504
r_dihedral_angle_1_deg7.756
r_scangle_it3.381
r_scbond_it2.15
r_angle_refined_deg1.659
r_mcangle_it1.239
r_mcbond_it0.742
r_symmetry_hbond_refined0.348
r_nbtor_refined0.316
r_nbd_refined0.225
r_xyhbond_nbd_refined0.179
r_symmetry_vdw_refined0.172
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms2437
Nucleic Acid Atoms
Solvent Atoms58
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing