7WAS

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7VB8 

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
2.7455.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.469α = 90
b = 96.469β = 90
c = 169.43γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2021-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9784SSRFBL19U1

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
12.40131.42199.80.1990.2040.0460.9157.519.53636336.78
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)
12.4012.4499.90.9550.9820.2280.8710.86.5

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-VALUE7vb82.40131.42136012189999.1380.190.18730.246243.738
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]
-0.756-0.378-0.7562.451
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.674
r_dihedral_angle_6_deg15.666
r_dihedral_angle_2_deg13.217
r_lrange_other12.921
r_lrange_it12.92
r_scangle_it10.395
r_scangle_other10.393
r_mcangle_it8.495
r_mcangle_other8.494
r_dihedral_angle_1_deg7.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.674
r_dihedral_angle_6_deg15.666
r_dihedral_angle_2_deg13.217
r_lrange_other12.921
r_lrange_it12.92
r_scangle_it10.395
r_scangle_other10.393
r_mcangle_it8.495
r_mcangle_other8.494
r_dihedral_angle_1_deg7.863
r_scbond_it7.747
r_scbond_other7.745
r_mcbond_other6.149
r_mcbond_it6.148
r_angle_refined_deg1.993
r_angle_other_deg0.651
r_symmetry_xyhbond_nbd_other0.257
r_nbd_other0.25
r_nbd_refined0.221
r_symmetry_nbd_refined0.215
r_xyhbond_nbd_refined0.205
r_symmetry_nbd_other0.19
r_nbtor_refined0.179
r_ncsr_local_group_10.129
r_chiral_restr0.091
r_symmetry_nbtor_other0.078
r_symmetry_xyhbond_nbd_refined0.077
r_bond_refined_d0.015
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5622
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms214

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing