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Crystal Structure of ANT(2")-Ia in complex with AMPCPP and gentamicin C1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CFS D_1000211507
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 295 100 mM MES, 30% PEG 200, 5% PEG 3000, 1mM MnCl2, 10 mM AMPCPP, 10mM gentamicin C1
Crystal Properties Matthews coefficient Solvent content 2.11 41.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.58 α = 90 b = 46.03 β = 90 c = 89 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD RIGAKU SATURN 944+ 2x2 binning 2015-03-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541780
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.49 46.03 99.7 0.056 0.014 31.1 17.2 27966 12.88
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.53 96.7 0.487 0.261 2.7 4.8 1968
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 FOURIER SYNTHESIS FREE R-VALUE D_1000211507 1.5 31.993 1.35 27371 1409 99.85 0.1487 0.1473 0.1588 0.1741 0.1845 Random selection 18.592
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 12.704 f_angle_d 1.755 f_chiral_restr 0.071 f_bond_d 0.017 f_plane_restr 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1379 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 85
Software Software Software Name Purpose PHENIX refinement StructureStudio data collection xia2 data scaling XSCALE data scaling XDS data reduction PDB_EXTRACT data extraction PHENIX phasing