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Crystal structure of the branched-chain polyamine synthase (BpsA) in complex with N4-aminopropylspermidine and 5-methylthioadenosine
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 100 mM sodium citrate tribasic dihydrate (pH 5.6),
2.5 M (w/v) 1,6-hexanediol
Crystal Properties Matthews coefficient Solvent content 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.533 α = 90 b = 50.978 β = 93.69 c = 402.428 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 100 CCD RAYONIX MX300HE 2014-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.84 50 99.8 0.061 27.7 5.2 241983
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 1.84 1.91 99.9 2.8 5.2
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 1.84 43.53 229853 12128 99.8 0.164 0.161 0.1685 0.207 0.2126 RANDOM 45.03
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] 0.36 0.04 0.27 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.863 r_dihedral_angle_4_deg 17.617 r_dihedral_angle_3_deg 16.48 r_dihedral_angle_1_deg 6.733 r_long_range_B_refined 6.594 r_long_range_B_other 6.57 r_scangle_other 4.718 r_scbond_it 3.029 r_scbond_other 3.028 r_mcangle_it 2.712
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.863 r_dihedral_angle_4_deg 17.617 r_dihedral_angle_3_deg 16.48 r_dihedral_angle_1_deg 6.733 r_long_range_B_refined 6.594 r_long_range_B_other 6.57 r_scangle_other 4.718 r_scbond_it 3.029 r_scbond_other 3.028 r_mcangle_it 2.712 r_mcangle_other 2.712 r_angle_refined_deg 2.283 r_mcbond_it 1.945 r_mcbond_other 1.944 r_angle_other_deg 1.267 r_chiral_restr 0.17 r_bond_refined_d 0.026 r_gen_planes_refined 0.013 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 19991 Nucleic Acid Atoms Solvent Atoms 1061 Heterogen Atoms 298
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing