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Crystal structure of the branched-chain polyamine synthase from Thermus thermophilus (Tth-BpsA) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q3M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Reservoir: 0.04 M sodium chloride , 0.04 M Tris pH 8.0, 27%(v/v) PEG 350MME
Crystal Properties Matthews coefficient Solvent content 2.08 41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.57 α = 90 b = 158.606 β = 118.95 c = 71.936 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 9M 2016-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.10000 SPring-8 BL32XU
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 1.66 50 99.3 15.1 5.3 156847
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 1.66 1.71
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 2Q3M 1.66 50 148976 7822 98.54 0.16918 0.16724 0.1814 0.20618 0.2172 RANDOM 28.17
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] -1.21 -0.44 3.28 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.32 r_dihedral_angle_4_deg 21.425 r_dihedral_angle_3_deg 15.133 r_long_range_B_refined 6.455 r_long_range_B_other 6.436 r_dihedral_angle_1_deg 5.782 r_scangle_other 5.219 r_scbond_it 3.422 r_scbond_other 3.421 r_mcangle_it 2.942
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.32 r_dihedral_angle_4_deg 21.425 r_dihedral_angle_3_deg 15.133 r_long_range_B_refined 6.455 r_long_range_B_other 6.436 r_dihedral_angle_1_deg 5.782 r_scangle_other 5.219 r_scbond_it 3.422 r_scbond_other 3.421 r_mcangle_it 2.942 r_mcangle_other 2.942 r_mcbond_it 2.165 r_mcbond_other 2.165 r_angle_refined_deg 1.92 r_angle_other_deg 1.099 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 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 10885 Nucleic Acid Atoms Solvent Atoms 688 Heterogen Atoms 231
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building MOLREP phasing