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Strictosidine Synthase from Ophiorrhiza pumila in complex with (S)-1-n-propyl-2,3,4,9-tetrahydro-1H-beta-carboline
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 0.1 M Tris-HCL pH 8.0, 0.3 M NH4Cl, 20% PEG 6K
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.365 α = 90 b = 78.756 β = 93.22 c = 62.213 γ = 90
Symmetry Space Group C 1 2 1
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 2016-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
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 1.9 54.84 98.9 0.05 0.04 1 7.5 4.1 28720
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 1.9 1.94 99.5 0.51 0.44 0.95 1.6 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 2FP9 1.9 54.84 27248 1472 98.87 0.2054 0.2033 0.2099 0.2433 0.2496 RANDOM 48.876
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] 3.61 -5.69 -0.45 -2.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.504 r_dihedral_angle_4_deg 20.875 r_dihedral_angle_3_deg 17.349 r_dihedral_angle_1_deg 8.015 r_angle_refined_deg 1.571 r_angle_other_deg 1.328 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.504 r_dihedral_angle_4_deg 20.875 r_dihedral_angle_3_deg 17.349 r_dihedral_angle_1_deg 8.015 r_angle_refined_deg 1.571 r_angle_other_deg 1.328 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2359 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing