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Crystal structure of TnmS3, an antibiotic binding protein from Streptomyces sp. CB03234
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 100 mM ammonium acetate, 100 mM bis-tris, and 17% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.63 α = 90 b = 67.82 β = 90 c = 83.868 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD ADSC QUANTUM 315r 2015-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 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 1.08 40 95.3 0.049 0.054 0.021 0.997 31.6 6.4 106971
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 1.08 1.1 88 0.62 0.691 0.298 0.794 1.9 4.8 4861
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 4HC5 1.08 40 101561 5344 95.07 0.18548 0.18456 0.1919 0.20301 0.2123 RANDOM 15.641
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] 0.34 -0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.771 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_4_deg 10.691 r_dihedral_angle_1_deg 5.943 r_long_range_B_refined 4.54 r_long_range_B_other 3.956 r_scangle_other 2.487 r_mcangle_it 1.658 r_mcangle_other 1.658 r_scbond_it 1.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.771 r_dihedral_angle_3_deg 11.809 r_dihedral_angle_4_deg 10.691 r_dihedral_angle_1_deg 5.943 r_long_range_B_refined 4.54 r_long_range_B_other 3.956 r_scangle_other 2.487 r_mcangle_it 1.658 r_mcangle_other 1.658 r_scbond_it 1.633 r_scbond_other 1.63 r_angle_refined_deg 1.427 r_mcbond_it 1.024 r_mcbond_other 1.023 r_angle_other_deg 0.908 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 1856 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOLREP phasing HKL-3000 data reduction HKL-3000 data scaling