☰ Navigation Tabs
TetR(D) in Complex with Tigecycline and Magnesium, co-crystallized
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 Protein: 10.0 mg/mL TetR(D), 0.2M NaCl, 50 mM Tris/HCl, pH 8.0, 2mM [TigeTC], 2mM MgCl2.
Precipitant: 1M (NH4)2SO4, 0.2M NaCl, 0.05M Tris/HCl, pH 8.0, 10mM MgCl2.
Protein/precipitant 2+2 microL, against 0.5mL Precipitant.
Crystal Properties Matthews coefficient Solvent content 2.77 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.49 α = 90 b = 68.49 β = 90 c = 179.25 γ = 90
Symmetry Space Group I 41 2 2
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 MARMOSAIC 225 mm CCD 2011-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.950000 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.85 50 98.2 0.05 0.05 33.95 14.15 18428 41
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 97.2 1.9 2.04 14.19
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2xpv 1.886 48.477 17367 880 98.219 0.215 0.2131 0.2205 0.2583 0.2611 37.603
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] 1.335 1.335 -2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.08 r_dihedral_angle_4_deg 22.541 r_dihedral_angle_3_deg 16.243 r_dihedral_angle_1_deg 6.634 r_lrange_it 5.631 r_lrange_other 5.631 r_scangle_it 4.03 r_scangle_other 4.03 r_mcangle_it 3.27 r_mcangle_other 3.269
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.08 r_dihedral_angle_4_deg 22.541 r_dihedral_angle_3_deg 16.243 r_dihedral_angle_1_deg 6.634 r_lrange_it 5.631 r_lrange_other 5.631 r_scangle_it 4.03 r_scangle_other 4.03 r_mcangle_it 3.27 r_mcangle_other 3.269 r_scbond_it 2.587 r_scbond_other 2.585 r_mcbond_it 2.22 r_mcbond_other 2.217 r_angle_refined_deg 1.982 r_angle_other_deg 1.539 r_nbd_other 0.242 r_nbd_refined 0.237 r_symmetry_xyhbond_nbd_refined 0.228 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.193 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.129 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.089 r_xyhbond_nbd_other 0.07 r_bond_refined_d 0.014 r_metal_ion_refined 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1550 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing