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Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) and spermidine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Ammonium acetate, PEG 2000MME
Crystal Properties Matthews coefficient Solvent content 1.95 37.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 176.567 α = 90 b = 57.256 β = 98.5 c = 54.485 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 PIXEL DECTRIS EIGER X 16M 2019-07-16 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 1.2 43.1 99.2 0.999 15.1 3.4 166200
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 1.2 1.22 0.778
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 7XIF 1.2 39.23 158009 8178 99.12 0.12066 0.11896 0.1218 0.15353 0.1563 RANDOM 21.381
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] -0.33 0.29 -0.67 0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.121 r_dihedral_angle_4_deg 17.911 r_dihedral_angle_3_deg 13.378 r_dihedral_angle_1_deg 6.568 r_rigid_bond_restr 5.169 r_scangle_other 4.919 r_long_range_B_refined 4.778 r_scbond_it 4.611 r_scbond_other 4.61 r_long_range_B_other 4.515
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.121 r_dihedral_angle_4_deg 17.911 r_dihedral_angle_3_deg 13.378 r_dihedral_angle_1_deg 6.568 r_rigid_bond_restr 5.169 r_scangle_other 4.919 r_long_range_B_refined 4.778 r_scbond_it 4.611 r_scbond_other 4.61 r_long_range_B_other 4.515 r_mcangle_it 2.381 r_mcangle_other 2.381 r_mcbond_other 2.114 r_mcbond_it 2.113 r_angle_refined_deg 2.045 r_angle_other_deg 1.595 r_chiral_restr 0.114 r_bond_refined_d 0.017 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4581 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling