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Crystal structure of AKRtyl-tylosin complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6OVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293.15 22% PEG 400, 0.1M MES
Crystal Properties Matthews coefficient Solvent content 2.8 61.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.021 α = 90 b = 111.021 β = 90 c = 560.041 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2021-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97915 SSRF BL18U1
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 2.25 50 100 0.13 0.991 11.3 6.8 317806 27.64
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 0.816 0.699 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.25 49.74 1.99 314585 15524 99 0.1828 0.181 0.1808 0.2165 0.2155 RANDOM 37.37
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 30.6648 f_angle_d 1.5824 f_chiral_restr 0.2873 f_bond_d 0.0116 f_plane_restr 0.0106
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 39036 Nucleic Acid Atoms Solvent Atoms 2147 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing