☰ Navigation Tabs
Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) alone or together with spermidine or thermospermine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ANX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Ammonium sulfate, Sodium citrate, PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.08 60.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 166.159 α = 90 b = 166.159 β = 90 c = 149.586 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 EIGER X 16M 2018-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.14 47.97 99.8 0.999 15.2 4.4 254276
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.14 2.18 0.526
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 3ANX 2.14 47.11 241370 12860 99.77 0.16176 0.16024 0.1446 0.1904 0.1699 RANDOM 46.18
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] 3.11 3.11 -6.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 16.048 r_long_range_B_other 10.445 r_long_range_B_refined 10.443 r_scangle_other 8.552 r_dihedral_angle_1_deg 6.886 r_mcangle_it 6.678 r_mcangle_other 6.678 r_scbond_it 6.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 20.009 r_dihedral_angle_3_deg 16.048 r_long_range_B_other 10.445 r_long_range_B_refined 10.443 r_scangle_other 8.552 r_dihedral_angle_1_deg 6.886 r_mcangle_it 6.678 r_mcangle_other 6.678 r_scbond_it 6.211 r_scbond_other 6.211 r_mcbond_it 5.286 r_mcbond_other 5.286 r_angle_refined_deg 1.597 r_angle_other_deg 1.386 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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 27332 Nucleic Acid Atoms Solvent Atoms 1206 Heterogen Atoms 332
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling