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Structure of Strictosidine Synthase, the Biosynthetic Entry to the Monoterpenoid Indole Alkaloid Family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 295 0.8M potassium sodium tartrate tetrahydrate, 100mM HEPES-Na, 2mM secologanin, pH 7.5, VAPOR DIFFUSION, temperature 295.0K
Crystal Properties Matthews coefficient Solvent content 3.64 66.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.607 α = 90 b = 148.607 β = 90 c = 121.069 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH double crystal Si[111] 2005-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8057 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 20 96 0.122 11.8 19913 19104 2 2 50
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.04 95 0.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT Native structure 3 20 2 19913 19104 787 100 0.193 0.1882 0.18606 0.1699 0.24 0.168 RANDOM 27.566
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] 4.62 2.31 4.62 -6.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.145 r_scangle_it 5.524 r_scbond_it 3.464 r_angle_refined_deg 1.833 r_mcangle_it 1.346 r_mcbond_it 0.685 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.145 r_scangle_it 5.524 r_scbond_it 3.464 r_angle_refined_deg 1.833 r_mcangle_it 1.346 r_mcbond_it 0.685 r_symmetry_vdw_refined 0.273 r_nbd_refined 0.256 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.118 r_symmetry_hbond_refined 0.104 r_bond_refined_d 0.02 r_gen_planes_refined 0.006 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 Atoms Number Protein Atoms 4764 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling MOLREP phasing