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Crystal structure of Agelastatin A bound to the 80S ribosome
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4V88
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 PEG 20K, KSCN, Mg Acetate, Tris-Acetate, Glycerol, Spermidine
Crystal Properties Matthews coefficient Solvent content 3.18 61.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 304.08 α = 90 b = 286.55 β = 99.05 c = 436.55 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2016-03-12 M SINGLE WAVELENGTH 2 1 x-ray PIXEL DECTRIS EIGER X 16M 2016-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 1.148 SOLEIL PROXIMA 1 2 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.5 98.383 100 0.567 0.597 0.985 5.56 10.553 925728 -3 71.28
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.5 3.6 99.9 2.259 2.425 0.322 1 7.424
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 4V88 3.5 98.383 1.35 925645 18297 99.97 0.1962 0.1953 0.1991 0.239 0.2402 79.7288
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 16.915 f_angle_d 1.13 f_chiral_restr 0.046 f_bond_d 0.007 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 178134 Nucleic Acid Atoms 222512 Solvent Atoms Heterogen Atoms 8952
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction PHASER phasing XDS data reduction