5G15

Structure Aurora A (122-403) bound to activating monobody Mb1 and AMPPCP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4C3RPDB ENTRIES 4C3R AND 3K2M
experimental modelPDB 3K2MPDB ENTRIES 4C3R AND 3K2M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5291AURORA A AND MONOBODIES WERE ALIQUOTED IN STORAGE BUFFER (20MM TRISHCL, 200MM NACL, 10% (V/V) GLYCEROL, 20MM MGCL2, 5MM TCEP, PH 7.50) AND KEPT AT -80C. AMPPCP WAS PREPARED FRESH FROM POWDER THE DAY OF CRYSTALLIZATION IN CONCENTRATIONS OF 100-120MM IN STORAGE BUFFER. CRYSTALS OF AURA IN COMPLEX WITH AMPPCP AND ACTIVATING MONOBODY, MB1, WERE OBTAINED BY COMBINING 0.5UL OF [300UM AURA WITH 5MM AMPPCP AND 300UM MB1] WITH 0.5UL OF MOTHER LIQUOR (0.1M MES SODIUM SALT PH 6.50, 0.2M AMMONIUM SULFATE, 4% (V/V) 1,3-PROPANEDIOL, 30% (W/V) PEG8000). CRYSTALS WERE GROWN AT 18C BY VAPOR DIFFUSION AND THE SITTING DROP METHOD. THE CRYSTALS WERE WASHED WITH MOTHER LIQUOR AND FLASH FROZEN IN LIQUID NITROGEN IN PREPARATION FOR DATA COLLECTION.
Crystal Properties
Matthews coefficientSolvent content
2.8657.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.339α = 90
b = 91.361β = 90
c = 143.715γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152015-05-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.2ALS8.2.2

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
12.0658.131000.1310.37.2308791.8
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)
12.062.1299.51.211.87.2

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 ENTRIES 4C3R AND 3K2M2.0677.129755105299.710.228530.226870.27388RANDOM34.133
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]
-0.020.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.402
r_dihedral_angle_3_deg16.379
r_dihedral_angle_4_deg14.611
r_dihedral_angle_1_deg7.235
r_mcangle_it4.45
r_scbond_it3.536
r_mcbond_it2.914
r_mcbond_other2.895
r_angle_refined_deg1.916
r_angle_other_deg1.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.402
r_dihedral_angle_3_deg16.379
r_dihedral_angle_4_deg14.611
r_dihedral_angle_1_deg7.235
r_mcangle_it4.45
r_scbond_it3.536
r_mcbond_it2.914
r_mcbond_other2.895
r_angle_refined_deg1.916
r_angle_other_deg1.046
r_chiral_restr0.107
r_bond_refined_d0.016
r_gen_planes_refined0.009
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2873
Nucleic Acid Atoms
Solvent Atoms145
Heterogen Atoms52

Software

Software
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
PHASERphasing
REFMACrefinement