5ARG

SMYD2 in complex with SGC probe BAY-598


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3TG5PDB ENTRY 3TG5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1727722% PEG 3350, 100 MMOL HEPES PH 7.0. CRYO BUFFER CONTAINS AN ADDTIONAL 20% GLYCEROL AND 1 MMOL LIGAND. OTHER CRYSTALISATION REMARKS:4 MILLIMOLAR COFACTOR SAM ADDED AND MIXTURE INCUBATED FOR 2 HOURS AT 4 DEGREE CELSIUS PRIOR TO CRYSTALLIZATION. CO- COMPLEX WITH BAY-598 FORMED BY SOAKING SMYD2-SAM CRYSTALS WITH 5 MILLIMOLAR LIGAND FOR 4 DAYS.
Crystal Properties
Matthews coefficientSolvent content
2.4549.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.343α = 90
b = 69.6β = 90
c = 131.115γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-01-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.1BESSY14.1

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
11.9948.6199.90.114.396.583365635.09
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)
11.992.1199.50.822.41

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 ENTRY 3TG51.9947.7231972168399.860.23220.230010.27318RANDOM55.525
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]
-2.240.052.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.541
r_dihedral_angle_3_deg18.929
r_dihedral_angle_4_deg17.422
r_dihedral_angle_1_deg6.604
r_scbond_it5.015
r_mcangle_it4.576
r_mcbond_it3.533
r_mcbond_other3.519
r_angle_refined_deg2.033
r_angle_other_deg0.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.541
r_dihedral_angle_3_deg18.929
r_dihedral_angle_4_deg17.422
r_dihedral_angle_1_deg6.604
r_scbond_it5.015
r_mcangle_it4.576
r_mcbond_it3.533
r_mcbond_other3.519
r_angle_refined_deg2.033
r_angle_other_deg0.9
r_chiral_restr0.099
r_bond_refined_d0.017
r_gen_planes_refined0.009
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_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 Atoms3428
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms71

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing