7VB8

SbSOMT in complex with resveratrol and nicotinamide adenine dinucleotide(NAD+)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherMrBUMP generated chimeric model

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62910.1 M sodium acetate pH 4.6, 0.2 M sodium acetate , 0.2 M ammonium chloride, 2.5% (w/v) polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
2.7455.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.831α = 90
b = 96.831β = 90
c = 168.038γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2020-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97853SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.7248.46299.80.060.0630.02130.219.49722522.6
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)
11.721.7597.10.9411.010.3570.8492.914.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUEMrBUMP generated chimeric model1.7248.46297159489999.8260.1650.16330.189326.372
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]
-0.735-0.367-0.7352.383
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.817
r_dihedral_angle_6_deg15.67
r_dihedral_angle_3_deg14.638
r_lrange_it8.15
r_lrange_other8.107
r_dihedral_angle_1_deg6.362
r_scangle_it6.057
r_scangle_other6.057
r_scbond_it4.125
r_scbond_other4.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.817
r_dihedral_angle_6_deg15.67
r_dihedral_angle_3_deg14.638
r_lrange_it8.15
r_lrange_other8.107
r_dihedral_angle_1_deg6.362
r_scangle_it6.057
r_scangle_other6.057
r_scbond_it4.125
r_scbond_other4.125
r_mcangle_it3.93
r_mcangle_other3.929
r_mcbond_it2.816
r_mcbond_other2.816
r_angle_refined_deg1.639
r_angle_other_deg0.558
r_nbd_refined0.225
r_nbd_other0.217
r_symmetry_nbd_other0.183
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.176
r_symmetry_nbd_refined0.167
r_symmetry_xyhbond_nbd_refined0.164
r_chiral_restr0.083
r_symmetry_nbtor_other0.075
r_bond_refined_d0.01
r_gen_planes_refined0.01
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5622
Nucleic Acid Atoms
Solvent Atoms568
Heterogen Atoms229

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERphasing