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Crystal structure of tetracycline destructase Tet(X7)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4A6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.2M ammonium sulfate and 20% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 3.1 60.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.13 α = 90 b = 131.97 β = 90 c = 136.97 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 100 CMOS RDI CMOS_8M 2018-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000033 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.55 19.77 99.5 0.09138 0.998 17.31 6.9 34444 50.63
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 2.55 2.641 0.8967 0.9762 0.3809 0.817 2.26
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4A6N 2.55 19.77 1.35 34427 1673 99.78 0.2088 0.207 0.2082 0.2434 0.2464 63.41
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.6138 f_angle_d 0.7166 f_chiral_restr 0.0464 f_bond_d 0.0038 f_plane_restr 0.0038
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5800 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 106
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing