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Crystal structure of TnmS2, an antibiotic binding protein from Streptomyces sp. CB03234
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 50 mM magnesium sulfate hydrate, 50 mM HEPES sodium, and 1.6 M lithium sulfate monohydrate
Crystal Properties Matthews coefficient Solvent content 2.68 54.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.298 α = 90 b = 74.298 β = 90 c = 342.783 γ = 120
Symmetry Space Group P 32 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 80 PIXEL DECTRIS PILATUS 6M 2016-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915, 0.97941 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.26 50 99.7 0.077 0.081 0.027 0.998 14.8 9 52843
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.31 99.8 0.0851 0.917 0.335 0.795 2.5 7.3 2585
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.27 50 48510 2536 97.47 0.20845 0.20548 0.26313 0.2643 RANDOM 36.19
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] -0.14 -0.07 -0.14 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.496 r_dihedral_angle_3_deg 16.792 r_dihedral_angle_4_deg 16.378 r_long_range_B_refined 10.294 r_long_range_B_other 10.294 r_scangle_other 8.166 r_dihedral_angle_1_deg 7.16 r_scbond_it 5.282 r_scbond_other 5.282 r_mcangle_it 5.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.496 r_dihedral_angle_3_deg 16.792 r_dihedral_angle_4_deg 16.378 r_long_range_B_refined 10.294 r_long_range_B_other 10.294 r_scangle_other 8.166 r_dihedral_angle_1_deg 7.16 r_scbond_it 5.282 r_scbond_other 5.282 r_mcangle_it 5.011 r_mcangle_other 5.01 r_mcbond_other 3.186 r_mcbond_it 3.185 r_angle_refined_deg 1.958 r_angle_other_deg 1.096 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6316 Nucleic Acid Atoms Solvent Atoms 291 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement AutoSol phasing HKL-3000 data reduction HKL-3000 data scaling