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Cryo X-ray structure of sisomicin bound AAC-VIa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BC6 PDB entry 6BC6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 285 17-25% PEG4000, 0.1 M sodium citrate, pH 5.6, 0.2 M ammonium acetate, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 2.3 46.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.55 α = 90 b = 78.55 β = 90 c = 83.604 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ 2016-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 50 98.7 0.089 9.1 2.9 26880 16.54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 96.3 0.532 2.8
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 PDB entry 6BC6 1.8 35.615 1.35 26876 1303 98.8 0.1508 0.1491 0.1493 0.1857 0.1858
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 21.421 f_angle_d 0.987 f_chiral_restr 0.065 f_bond_d 0.009 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2028 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement SCALEPACK data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHASER phasing