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Shewanella oneidensis MR-1 Toxin Antitoxin System HipA, HipB and its operator DNA complex (space group P21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DNV PDB ENTRY 3DNV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.2 M calcium acetate hydrate, pH 7.5, 20% PEG3350, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.45 49.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.24 α = 90 b = 57.33 β = 95.81 c = 171.38 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 200 PIXEL DECTRIS PILATUS 6M 2013-03-12 M SINGLE WAVELENGTH 2 1 x-ray PIXEL DECTRIS PILATUS 2M-F 2012-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1 PETRA III, EMBL c/o DESY P13 (MX1) 2 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1,2 3.786 47.573 97.03 13858 1.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 3.786
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 3DNV 3.786 47.573 1.99 13855 693 97.01 0.2399 0.2364 0.2551 0.3064 0.3179
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 16.804 f_angle_d 0.946 f_chiral_restr 0.035 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7760 Nucleic Acid Atoms 1003 Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing PHENIX refinement XDS data reduction XDS data scaling