2FPC

Structure of Strictosidine Synthase, the Biosynthetic Entry to the Monoterpenoid Indole Alkaloid Family


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNative structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION7.52950.8M potassium sodium tartrate tetrahydrate, 100mM HEPES-Na, 2mM secologanin, pH 7.5, VAPOR DIFFUSION, temperature 295.0K
Crystal Properties
Matthews coefficientSolvent content
3.6466.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 148.607α = 90
b = 148.607β = 90
c = 121.069γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHdouble crystal Si[111]2005-11-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8057EMBL/DESY, HAMBURGX11

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
1320960.12211.819913191042250
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)
133.04950.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTNative structure320219913191047871000.1930.18820.186060.24RANDOM27.566
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]
4.622.314.62-6.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.145
r_scangle_it5.524
r_scbond_it3.464
r_angle_refined_deg1.833
r_mcangle_it1.346
r_mcbond_it0.685
r_symmetry_vdw_refined0.273
r_nbd_refined0.256
r_xyhbond_nbd_refined0.196
r_chiral_restr0.118
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.145
r_scangle_it5.524
r_scbond_it3.464
r_angle_refined_deg1.833
r_mcangle_it1.346
r_mcbond_it0.685
r_symmetry_vdw_refined0.273
r_nbd_refined0.256
r_xyhbond_nbd_refined0.196
r_chiral_restr0.118
r_symmetry_hbond_refined0.104
r_bond_refined_d0.02
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4764
Nucleic Acid Atoms
Solvent Atoms102
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing