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Strictosidine Synthase from Catharanthus roseus in complex with racemic 1-methyl-2,3,4,9-tetrahydro-1H-beta-carboline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6S5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 0.2 M sodium chloride, HEPES pH 7.0, 20%
PEG 6000 (w/v)
Crystal Properties Matthews coefficient Solvent content 2.43 49.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.44 α = 90 b = 71.42 β = 90 c = 109.58 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 PIXEL DECTRIS EIGER2 XE 16M 2017-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97949 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.54 43.47 99 0.05 0.03 1 14.1 6.4 51780
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.58 1.1 0.7 0.58 1.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 6S5M 1.54 43.47 49104 2618 98.6 0.1839 0.1821 0.1964 0.2176 0.2312 RANDOM 34.283
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] -1.52 -1.19 2.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.742 r_dihedral_angle_4_deg 19.392 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 7.073 r_angle_refined_deg 2.157 r_angle_other_deg 1.228 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.742 r_dihedral_angle_4_deg 19.392 r_dihedral_angle_3_deg 13.422 r_dihedral_angle_1_deg 7.073 r_angle_refined_deg 2.157 r_angle_other_deg 1.228 r_chiral_restr 0.146 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2401 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing