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Crystal structure of AtS13 from Actinomadura melliaura
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 3.5 M sodium formate pH 7.0, cryoprotected by adding 20% glycerol
Crystal Properties Matthews coefficient Solvent content 3.98 69.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 233.149 α = 90 b = 233.149 β = 90 c = 460.859 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 CCD MARMOSAIC 225 mm CCD 2014-10-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.98 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 3 30 100 0.138 0.146 0.146 0.054 4.1 10.2 95972 87.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.05 100 0.726 0.483 9.5 4750
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4RXK 3.0012 29.953 1.34 95912 1999 99.9 0.188 0.1873 0.1884 0.2201 0.2185 Random selection 109.5
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 12.888 f_angle_d 1.197 f_chiral_restr 0.065 f_bond_d 0.014 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20446 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 16
Software Software Software Name Purpose HKL-2000 data reduction PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data scaling PHENIX phasing