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Rauvolfia serpentina strictosidine synthase (RsSTR) in complex with a non-reactive tryptamine substitute crystallized in P1211 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V1S Dimer
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2 M Sodium chloride, 0.1 M Tris pH 8.5, 25% w/v Polyethylene glycol 3,350
Crystal Properties Matthews coefficient Solvent content 2.34 47.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.49 α = 90 b = 82.64 β = 98.52 c = 171.84 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2022-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54179
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.67 26.429 99.9 0.108 0.121 0.054 0.996 11.2 4.9 69947
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) Redundancy Number Unique Reflections (All) 1 2.67 2.73 100 0.661 0.739 0.326 0.794 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.67 26.429 69933 3459 99.871 0.197 0.1956 0.2012 0.2177 0.2236 RANDOM 47.873
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] 0.057 -1.431 0.185 0.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.273 r_dihedral_angle_6_deg 13.13 r_dihedral_angle_1_deg 7.453 r_dihedral_angle_2_deg 5.926 r_lrange_it 3.735 r_lrange_other 3.734 r_scangle_it 1.738 r_scangle_other 1.738 r_mcangle_it 1.629 r_mcangle_other 1.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.273 r_dihedral_angle_6_deg 13.13 r_dihedral_angle_1_deg 7.453 r_dihedral_angle_2_deg 5.926 r_lrange_it 3.735 r_lrange_other 3.734 r_scangle_it 1.738 r_scangle_other 1.738 r_mcangle_it 1.629 r_mcangle_other 1.629 r_scbond_it 1.032 r_scbond_other 1.032 r_angle_refined_deg 0.991 r_mcbond_it 0.94 r_mcbond_other 0.94 r_angle_other_deg 0.367 r_symmetry_nbd_refined 0.26 r_nbd_other 0.243 r_symmetry_xyhbond_nbd_refined 0.223 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.193 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.178 r_symmetry_nbtor_other 0.08 r_ncsr_local_group_7 0.076 r_ncsr_local_group_16 0.073 r_ncsr_local_group_3 0.072 r_ncsr_local_group_13 0.072 r_ncsr_local_group_14 0.07 r_ncsr_local_group_25 0.07 r_ncsr_local_group_26 0.07 r_ncsr_local_group_5 0.069 r_ncsr_local_group_11 0.068 r_ncsr_local_group_21 0.068 r_ncsr_local_group_23 0.068 r_ncsr_local_group_28 0.068 r_ncsr_local_group_8 0.067 r_ncsr_local_group_15 0.067 r_ncsr_local_group_18 0.067 r_ncsr_local_group_19 0.067 r_ncsr_local_group_22 0.066 r_ncsr_local_group_1 0.065 r_ncsr_local_group_4 0.063 r_ncsr_local_group_12 0.063 r_ncsr_local_group_9 0.061 r_ncsr_local_group_20 0.061 r_ncsr_local_group_10 0.059 r_ncsr_local_group_24 0.059 r_ncsr_local_group_27 0.059 r_chiral_restr 0.057 r_ncsr_local_group_2 0.056 r_ncsr_local_group_6 0.049 r_ncsr_local_group_17 0.049 r_bond_refined_d 0.018 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_chiral_restr_other 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19065 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing