6GRA | pdb_00006gra

Human AURKA bound to BRD-7880


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J4Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.2 M potassium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% PEG 3350, 10% ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.652.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.169α = 90
b = 83.169β = 90
c = 171.852γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 R CdTe 300K2013-09-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)CC (Half)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
12.685.931000.070.99913.38.611497
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.741000.8182.48.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2J4Z2.666.521087754899.780.212770.210050.210.268590.27RANDOM75.206
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]
-0.94-0.47-0.943.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.035
r_dihedral_angle_4_deg19.825
r_dihedral_angle_3_deg16.656
r_dihedral_angle_1_deg7.865
r_long_range_B_refined4.769
r_long_range_B_other4.769
r_scangle_other3.273
r_mcangle_other2.847
r_mcangle_it2.846
r_scbond_it2.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.035
r_dihedral_angle_4_deg19.825
r_dihedral_angle_3_deg16.656
r_dihedral_angle_1_deg7.865
r_long_range_B_refined4.769
r_long_range_B_other4.769
r_scangle_other3.273
r_mcangle_other2.847
r_mcangle_it2.846
r_scbond_it2.076
r_scbond_other2.076
r_mcbond_it1.79
r_mcbond_other1.787
r_angle_refined_deg1.291
r_angle_other_deg0.835
r_chiral_restr0.269
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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 Atoms1976
Nucleic Acid Atoms
Solvent Atoms3
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing