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Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other apo PCY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 PCY1-S562A complex with PresegA1 was crystallized at 13.3 mg/mL with 0.163 mM PresegA1 in 28% (w/v) PEG 5000 MME, 140 mM Mg acetate tetrahydrate and 0.1 M Tris pH 7.5. For cryo protection 7% (v/v) glycerol were added to reservoir solution.
Crystal Properties Matthews coefficient Solvent content 2.21 44.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.08 α = 93 b = 88.6 β = 99.32 c = 144.95 γ = 90.05
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2016-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.920 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2 77.07 97 4.8 1.8 183511
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 apo PCY1 2 77.07 183511 9515 96.97 0.22296 0.22126 0.2273 0.25625 0.2617 RANDOM 38.259
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] 1.5 -0.22 -0.38 -0.96 -0.01 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 17.007 r_dihedral_angle_3_deg 13.936 r_dihedral_angle_1_deg 6.883 r_long_range_B_other 5.911 r_long_range_B_refined 5.91 r_scangle_other 2.985 r_mcangle_it 2.871 r_mcangle_other 2.871 r_angle_other_deg 2.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.387 r_dihedral_angle_4_deg 17.007 r_dihedral_angle_3_deg 13.936 r_dihedral_angle_1_deg 6.883 r_long_range_B_other 5.911 r_long_range_B_refined 5.91 r_scangle_other 2.985 r_mcangle_it 2.871 r_mcangle_other 2.871 r_angle_other_deg 2.073 r_scbond_it 1.92 r_scbond_other 1.92 r_mcbond_it 1.835 r_mcbond_other 1.835 r_angle_refined_deg 1.64 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23045 Nucleic Acid Atoms Solvent Atoms 844 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing