3V1S

Scaffold tailoring by a newly detected Pictet-Spenglerase ac-tivity of strictosidine synthase (STR1): from the common tryp-toline skeleton to the rare piperazino-indole framework


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V91PDB ENTRY 2V91

Crystallization

Crystal Properties
Matthews coefficientSolvent content
3.7266.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 150.976α = 90
b = 150.976β = 90
c = 121.471γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.3244.599.644490722

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 2V912.32844.4962.0144082220499.640.18690.18470.2296random51.6125
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]
-0.2427-0.24270.4854
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d13.524
f_angle_d1.109
f_chiral_restr0.077
f_bond_d0.008
f_plane_restr0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4764
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms24

Software

Software
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction