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Binary (paromomycin) structure of AAC-IIIb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6BC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 1-3% PEG 4000, 20-25% isopropanol and 0.1M HEPES, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.87 68.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.19 α = 90 b = 106.19 β = 90 c = 69 γ = 120
Symmetry Space Group P 32 2 1
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 S 6M 2018-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 2.2 38.26 97.3 0.07 0.087 0.051 0.996 9.8 2.6 22425 34.32
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 2.2 2.27 98.1 0.513 0.646 0.388 0.772 2.6
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 THROUGHOUT 6BC3 2.2 38.264 1.34 22380 1187 96.74 0.2022 0.2002 0.2026 0.2367 0.2372 42.0477
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1990 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 42
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction MOSFLM data reduction PHASER phasing