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Crystal structure of the branched-chain polyamine synthase C9 mutein from Thermus thermophilus (Tth-BpsA C9) in complex with N4-aminopropylspermidine and 5'-methylthioadenosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Reservoir 0.02 M sodium chloride, 0.05 M MES pH 5.5, 14%(v/v) PEG 350MME
Crystal Properties Matthews coefficient Solvent content 2.09 41.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.777 α = 90 b = 158.518 β = 118.94 c = 72.018 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 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 1.9 50 99.2 19.6 6.7 106347
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 1.9 1.97
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.9 49.33 101022 5285 99.61 0.20254 0.19987 0.2067 0.25409 0.2602 RANDOM 24.109
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_4_deg 18.593 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.624 r_long_range_B_refined 5.415 r_long_range_B_other 5.415 r_scangle_other 3.845 r_mcangle_it 2.686 r_mcangle_other 2.686 r_scbond_other 2.448
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.211 r_dihedral_angle_4_deg 18.593 r_dihedral_angle_3_deg 15.165 r_dihedral_angle_1_deg 6.624 r_long_range_B_refined 5.415 r_long_range_B_other 5.415 r_scangle_other 3.845 r_mcangle_it 2.686 r_mcangle_other 2.686 r_scbond_other 2.448 r_scbond_it 2.447 r_angle_refined_deg 1.907 r_mcbond_it 1.852 r_mcbond_other 1.851 r_angle_other_deg 1.222 r_chiral_restr 0.118 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 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 10912 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 174
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Coot model building PHASER phasing