6GR9 | pdb_00006gr9

Human AURKC INCENP complex bound to VX-680


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6GR8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.527720 % PEG3350, 10 % ethylene glycol, 0.1 M bis-tris-propane pH 7.5, 0.2 M sodium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.9558.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.617α = 90
b = 82.617β = 90
c = 121γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 R CdTe 300K2014-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.2571.551000.070.99914.85.223264
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)
12.252.321000.68924.9

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 REPLACEMENTTHROUGHOUT6GR82.2571.5522049117799.90.183790.181650.190.224430.23RANDOM44.179
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]
-0.38-0.19-0.381.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.256
r_dihedral_angle_4_deg23.903
r_dihedral_angle_3_deg16.685
r_long_range_B_refined7.643
r_long_range_B_other7.557
r_dihedral_angle_1_deg6.465
r_scangle_other5.648
r_mcangle_it4.499
r_mcangle_other4.498
r_scbond_it3.548
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.256
r_dihedral_angle_4_deg23.903
r_dihedral_angle_3_deg16.685
r_long_range_B_refined7.643
r_long_range_B_other7.557
r_dihedral_angle_1_deg6.465
r_scangle_other5.648
r_mcangle_it4.499
r_mcangle_other4.498
r_scbond_it3.548
r_scbond_other3.533
r_mcbond_other2.97
r_mcbond_it2.969
r_angle_refined_deg1.329
r_angle_other_deg0.824
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
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 Atoms2605
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing