6G39

Crystal structure of haspin F605Y mutant 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
3.0459.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.82α = 90
b = 78.99β = 90
c = 79.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2015-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

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
11.4522.0198.30.060.99714.25.486860
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)
11.451.5396.90.570.80135.4

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 REPLACEMENTTHROUGHOUT4OUC1.4522.0182433437698.040.158560.157620.17543RANDOM25.173
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]
0.41-0.680.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.181
r_sphericity_bonded15.665
r_dihedral_angle_4_deg13.476
r_dihedral_angle_3_deg12.209
r_dihedral_angle_1_deg6.494
r_long_range_B_refined6.478
r_long_range_B_other6.477
r_scangle_other2.645
r_scbond_it1.66
r_scbond_other1.659
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.181
r_sphericity_bonded15.665
r_dihedral_angle_4_deg13.476
r_dihedral_angle_3_deg12.209
r_dihedral_angle_1_deg6.494
r_long_range_B_refined6.478
r_long_range_B_other6.477
r_scangle_other2.645
r_scbond_it1.66
r_scbond_other1.659
r_angle_refined_deg1.644
r_mcangle_other1.426
r_mcangle_it1.423
r_angle_other_deg0.94
r_mcbond_it0.908
r_mcbond_other0.898
r_chiral_restr0.105
r_bond_refined_d0.015
r_gen_planes_refined0.01
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2628
Nucleic Acid Atoms
Solvent Atoms339
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing