5DNR

Aurora A Kinase in complex with ATP in space group P41212


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FDN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292100 mM HEPES, 200 mM magnesium sulfate, 2-20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.6165.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.46α = 90
b = 81.46β = 90
c = 137.38γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

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
11.9557.699.90.05427.712.93460835.38
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)
11.95299.80.674.213.5

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 REPLACEMENTTHROUGHOUT3FDN1.9518.2232728165299.740.206420.20550.22552RANDOM40.296
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.767
r_dihedral_angle_4_deg17.429
r_dihedral_angle_3_deg14.491
r_long_range_B_other11.108
r_long_range_B_refined11.084
r_scangle_other9.805
r_scbond_it7.344
r_scbond_other7.341
r_mcangle_other4.063
r_mcangle_it3.942
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.767
r_dihedral_angle_4_deg17.429
r_dihedral_angle_3_deg14.491
r_long_range_B_other11.108
r_long_range_B_refined11.084
r_scangle_other9.805
r_scbond_it7.344
r_scbond_other7.341
r_mcangle_other4.063
r_mcangle_it3.942
r_dihedral_angle_1_deg3.793
r_angle_other_deg3.673
r_mcbond_it3.153
r_mcbond_other2.762
r_angle_refined_deg1.694
r_chiral_restr0.095
r_gen_planes_other0.023
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2173
Nucleic Acid Atoms
Solvent Atoms120
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling