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Crystal structure of the branched-chain polyamine synthase from Thermococcus kodakarensis (Tk-BpsA) in complex with N4-bis(aminopropyl)spermidine and 5'-methylthioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XNC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 Reservoir: 0.015 M tricine pH 8.5, 24%(v/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 1.98 37.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.17 α = 90 b = 74.17 β = 90 c = 105.934 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 100 PIXEL DECTRIS PILATUS3 6M 2017-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 50 100 26.1 10.1 44104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07
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 5XNC 2 40.87 41889 2182 99.91 0.19753 0.19603 0.1994 0.22769 0.2308 RANDOM 32.088
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] 0.01 0.01 0.01 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_dihedral_angle_3_deg 12.51 r_dihedral_angle_4_deg 12.32 r_dihedral_angle_1_deg 5.626 r_long_range_B_refined 2.162 r_long_range_B_other 2.077 r_angle_refined_deg 1.136 r_scangle_other 0.999 r_mcangle_it 0.942 r_mcangle_other 0.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.659 r_dihedral_angle_3_deg 12.51 r_dihedral_angle_4_deg 12.32 r_dihedral_angle_1_deg 5.626 r_long_range_B_refined 2.162 r_long_range_B_other 2.077 r_angle_refined_deg 1.136 r_scangle_other 0.999 r_mcangle_it 0.942 r_mcangle_other 0.941 r_angle_other_deg 0.873 r_scbond_it 0.572 r_scbond_other 0.572 r_mcbond_it 0.536 r_mcbond_other 0.536 r_chiral_restr 0.056 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5712 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building PHASER phasing