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Strictosidine Synthase from Ophiorrhiza pumila in complex with N-[2-(1H-Indol-3-yl)ethyl]-3-methyl-1-butanamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 20% PEG 6000; 0.3 M MH4Cl; 0.1M Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.747 α = 90 b = 125.747 β = 90 c = 117.081 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 120 PIXEL DECTRIS PILATUS 6M-F 2017-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
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 2.03 39.9 99.7 0.19 0.12 0.99 6.8 5.1 133410
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 2.03 2.06 0.67 0.44 0.97 2.9
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 2FP9 2.03 39.9 126761 6605 99.65 0.313 0.3119 0.3154 0.3338 0.3359 RANDOM 16.832
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] -1.18 -0.59 -1.18 3.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.919 r_dihedral_angle_3_deg 14.091 r_dihedral_angle_4_deg 13.565 r_dihedral_angle_1_deg 7.622 r_angle_refined_deg 1.476 r_angle_other_deg 1.177 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.919 r_dihedral_angle_3_deg 14.091 r_dihedral_angle_4_deg 13.565 r_dihedral_angle_1_deg 7.622 r_angle_refined_deg 1.476 r_angle_other_deg 1.177 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13970 Nucleic Acid Atoms Solvent Atoms 711 Heterogen Atoms 221
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing