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Crystal structure of the aminopropyltransferase, SpeE from hyperthermophilic crenarchaeon, Pyrobaculum calidifontis in complex with 5'-methylthioadenosine (MTA) and spermine
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 Sodium formate, HEPES, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.09 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.828 α = 72.46 b = 80.392 β = 89.13 c = 97.844 γ = 88.08
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 2018-10-21 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 2.25 46.65 99.5 0.989 5.4 3.6 106737
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 2.25 2.29 0.813
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 2.25 46.69 100802 5275 98.87 0.17442 0.17272 0.1762 0.20743 0.2112 RANDOM 47.308
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] 0.58 -0.29 0.4 -0.7 -0.94 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.48 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 16.899 r_long_range_B_refined 10.175 r_dihedral_angle_1_deg 6.368 r_scbond_it 5.963 r_mcangle_it 5.246 r_mcbond_it 3.861 r_angle_refined_deg 1.467 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.48 r_dihedral_angle_4_deg 19.72 r_dihedral_angle_3_deg 16.899 r_long_range_B_refined 10.175 r_dihedral_angle_1_deg 6.368 r_scbond_it 5.963 r_mcangle_it 5.246 r_mcbond_it 3.861 r_angle_refined_deg 1.467 r_chiral_restr 0.102 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18268 Nucleic Acid Atoms Solvent Atoms 765 Heterogen Atoms 302
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building Aimless data scaling