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Crystal structure of triamine/agmatine aminopropyltransferase (SPEE) from thermus thermophilus, complexed with MTA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 1.8M AMMONIUM SULFATE, 0.1M MES, 1MM SAM, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.56 52.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.04 α = 90 b = 88.04 β = 90 c = 191 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.5 20 96.7 0.119 25838
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 1UIR 2.5 20 22098 2419 91.7 0.188 0.18 0.1799 0.263 0.2622 RANDOM 40.93
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] -0.98 -0.98 1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.833 r_dihedral_angle_3_deg 22.876 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_1_deg 9.019 r_scangle_it 5.005 r_scbond_it 3.359 r_angle_refined_deg 2.686 r_mcangle_it 2.204 r_mcbond_it 1.29 r_symmetry_hbond_refined 0.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.833 r_dihedral_angle_3_deg 22.876 r_dihedral_angle_4_deg 18.528 r_dihedral_angle_1_deg 9.019 r_scangle_it 5.005 r_scbond_it 3.359 r_angle_refined_deg 2.686 r_mcangle_it 2.204 r_mcbond_it 1.29 r_symmetry_hbond_refined 0.488 r_nbtor_refined 0.348 r_nbd_refined 0.292 r_symmetry_vdw_refined 0.276 r_xyhbond_nbd_refined 0.224 r_chiral_restr 0.162 r_bond_refined_d 0.03 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5065 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 40
Software Software Software Name Purpose MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling