☰ Navigation Tabs
Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with hexylthio-DADMe-Immucillin-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4WKN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 295 100 mM Bis-Tris pH 5.5, 200 mM Magnesium Chloride, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 40.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.367 α = 87.54 b = 75.288 β = 89.05 c = 90.437 γ = 71.13
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 MX-225 2017-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
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 1.7 90.35 97.3 0.99 8.1 4.2 179940
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 1.7 1.73 95.7 0.84 2.1 4.3
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 4WKN 1.7 90.35 171111 8797 97.33 0.23119 0.23033 0.2369 0.24786 0.2522 RANDOM 23.148
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] -0.32 -0.64 0.06 0.19 0.07 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.144 r_dihedral_angle_4_deg 23.054 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 6.253 r_long_range_B_refined 4.375 r_long_range_B_other 4.375 r_scangle_other 2.103 r_mcangle_it 1.796 r_mcangle_other 1.796 r_angle_refined_deg 1.334
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.144 r_dihedral_angle_4_deg 23.054 r_dihedral_angle_3_deg 13.647 r_dihedral_angle_1_deg 6.253 r_long_range_B_refined 4.375 r_long_range_B_other 4.375 r_scangle_other 2.103 r_mcangle_it 1.796 r_mcangle_other 1.796 r_angle_refined_deg 1.334 r_scbond_it 1.256 r_scbond_other 1.256 r_mcbond_it 1.034 r_mcbond_other 1.034 r_angle_other_deg 0.894 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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 14049 Nucleic Acid Atoms Solvent Atoms 1710 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing