6G34

Crystal structure of haspin in complex with 5-iodotubercidin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4OUC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP277.1551-63% MPD and 0.1M SPG buffer, pH 6.0-6.5
Crystal Properties
Matthews coefficientSolvent content
3.0359.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.58α = 90
b = 78.74β = 90
c = 79.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2014-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9794DiamondI02

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
11.7623.9898.10.0870.99413.96.248665
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.7996.80.2240.9687.26.5

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 REPLACEMENTTHROUGHOUT4OUC1.7623.9846249237397.750.140120.138330.17374RANDOM21.753
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]
0.21-0.680.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.903
r_dihedral_angle_4_deg17.734
r_dihedral_angle_3_deg12.002
r_sphericity_free8.303
r_sphericity_bonded6.771
r_dihedral_angle_1_deg6.433
r_rigid_bond_restr5.783
r_long_range_B_other2.504
r_long_range_B_refined2.501
r_scangle_other2.369
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.903
r_dihedral_angle_4_deg17.734
r_dihedral_angle_3_deg12.002
r_sphericity_free8.303
r_sphericity_bonded6.771
r_dihedral_angle_1_deg6.433
r_rigid_bond_restr5.783
r_long_range_B_other2.504
r_long_range_B_refined2.501
r_scangle_other2.369
r_scbond_it2.116
r_scbond_other2.096
r_mcangle_it1.872
r_mcangle_other1.871
r_angle_refined_deg1.75
r_mcbond_other1.551
r_mcbond_it1.547
r_angle_other_deg1.022
r_chiral_restr0.118
r_bond_refined_d0.017
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2588
Nucleic Acid Atoms
Solvent Atoms229
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing