5DRD

Aurora A Kinase in Complex with ATP in Space Group P6122


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4292100 mM HEPES pH 7.4, 200 mM magnesium sulfate, 2-20% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.6653.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.61α = 90
b = 81.61β = 90
c = 166.45γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9184DiamondI03

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
12.1370.681000.08917.918.419152
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)
12.132.191001.773219.4

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 REPLACEMENTFREE R-VALUE3FDN2.1370.681812396599.990.208620.205920.26163RANDOM59.809
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]
0.120.060.12-0.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.21
r_dihedral_angle_4_deg18.811
r_dihedral_angle_3_deg18.593
r_long_range_B_refined10.525
r_long_range_B_other10.523
r_scangle_other8.678
r_dihedral_angle_1_deg6.827
r_mcangle_it6.655
r_mcangle_other6.654
r_scbond_it6.058
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.21
r_dihedral_angle_4_deg18.811
r_dihedral_angle_3_deg18.593
r_long_range_B_refined10.525
r_long_range_B_other10.523
r_scangle_other8.678
r_dihedral_angle_1_deg6.827
r_mcangle_it6.655
r_mcangle_other6.654
r_scbond_it6.058
r_scbond_other6.055
r_mcbond_it4.939
r_mcbond_other4.931
r_angle_refined_deg1.981
r_angle_other_deg1.044
r_chiral_restr0.097
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms2120
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
PHASERphasing
XDSdata reduction
XDSdata scaling