3OXG

human lysine methyltransferase Smyd3 in complex with AdoHcy (Form III)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3OXF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP927720% polyethylene glycol monomethyl ether 550, 0.1M NaCl, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.2762.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 103.439α = 90
b = 103.439β = 90
c = 112.202γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2010-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97908SSRFBL17U

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
13.45099.90.137.49395
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)
13.43.521000.6492.55.9

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3OXF3.4150935348799.650.22530.22390.2493RANDOM97.4365
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]
-1.08-0.54-1.081.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.669
r_dihedral_angle_4_deg17.355
r_dihedral_angle_3_deg17.2
r_dihedral_angle_1_deg4.919
r_scangle_it1.143
r_angle_refined_deg1.095
r_mcangle_it0.83
r_scbond_it0.631
r_mcbond_it0.478
r_chiral_restr0.071
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.669
r_dihedral_angle_4_deg17.355
r_dihedral_angle_3_deg17.2
r_dihedral_angle_1_deg4.919
r_scangle_it1.143
r_angle_refined_deg1.095
r_mcangle_it0.83
r_scbond_it0.631
r_mcbond_it0.478
r_chiral_restr0.071
r_bond_refined_d0.008
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3397
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing