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Crystal structure of TnmS1, 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 6.5 298 50 mM ammonium sulphate, 50 mM bis-tris propane, and 30 % v/v pentaerythriol ethoxylate (15/4 EO/OH)
Crystal Properties Matthews coefficient Solvent content 1.94 36.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.569 α = 90 b = 66.124 β = 90 c = 103.354 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 80 CCD ADSC QUANTUM 315r 2015-11-07 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 1.95 50 98.4 0.071 0.074 0.02 0.999 33 13.1 18652
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 1.95 1.98 97.2 0.761 0.802 0.242 0.88 2.4 9.6 890
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 1.95 50 16523 898 91.91 0.19843 0.19546 0.2037 0.25621 0.2604 RANDOM 23.311
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] 0.08 0.16 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.142 r_dihedral_angle_4_deg 15.949 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 7.377 r_long_range_B_refined 5.181 r_long_range_B_other 5.085 r_mcangle_it 2.765 r_mcangle_other 2.765 r_scangle_other 2.67 r_mcbond_it 1.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.142 r_dihedral_angle_4_deg 15.949 r_dihedral_angle_3_deg 15.107 r_dihedral_angle_1_deg 7.377 r_long_range_B_refined 5.181 r_long_range_B_other 5.085 r_mcangle_it 2.765 r_mcangle_other 2.765 r_scangle_other 2.67 r_mcbond_it 1.583 r_mcbond_other 1.577 r_scbond_it 1.559 r_scbond_other 1.557 r_angle_refined_deg 1.449 r_angle_other_deg 0.951 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 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 2000 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOLREP phasing HKL-3000 data reduction HKL-3000 data scaling