5CCL

Crystal structure of SMYD3 with SAM and oxindole compound


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.10 M Magnesium formate, 0.1M Tris 8.0, 14% w/v PEG 3350. Crystals of SMYD3-SAM were produced and compound was soaked into the pre-formed crystals
Crystal Properties
Matthews coefficientSolvent content
2.0740.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.594α = 90
b = 65.232β = 90
c = 105.966γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97907SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.555.5594.40.0690.0770.03314.6562186
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.51.5598.60.2260.2530.1110.9484.96399

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.555.5559053308194.290.11590.11340.1643RANDOM22.997
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]
0.61-0.56-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.614
r_sphericity_free23.573
r_dihedral_angle_4_deg19.865
r_dihedral_angle_3_deg14.196
r_sphericity_bonded11.646
r_dihedral_angle_1_deg6.11
r_mcangle_it3.787
r_mcbond_it3.367
r_mcbond_other3.367
r_rigid_bond_restr3.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.614
r_sphericity_free23.573
r_dihedral_angle_4_deg19.865
r_dihedral_angle_3_deg14.196
r_sphericity_bonded11.646
r_dihedral_angle_1_deg6.11
r_mcangle_it3.787
r_mcbond_it3.367
r_mcbond_other3.367
r_rigid_bond_restr3.323
r_angle_refined_deg1.732
r_angle_other_deg0.913
r_chiral_restr0.124
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3400
Nucleic Acid Atoms
Solvent Atoms449
Heterogen Atoms73

Software

Software
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction