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Structure of the Thermotoga maritima HK853-BeF3-RR468 complex at pH 5.0
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DGE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 1:1 mixture of protein solution with mother liquor solution;
Protein solution contains:
10 mg/mL HK853cp,
7.5 mg/mL RR468,
10 mM Tris (pH 8.0),
7 mM MgCl2,
5 mM BeCl2,
30 mM NaF,
4 mM AMPPNP.
Mother liquor solution contains:
0.1 M citric acid (pH 4.0),
0.8 M ammonium sulfate.
Adjust final pH to 5.0.
Crystal Properties Matthews coefficient Solvent content 3.4 63.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.97 α = 90 b = 98.38 β = 110.54 c = 72.05 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 300 mm CCD 2015-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.68 49.19 99.8 0.076 20.6 7.7 32777
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.75 87.5 0.875
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 3dge 2.68 49.19 1.38 32763 1660 99.96 0.1842 0.1822 0.1936 0.2218 0.2336
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 12.558 f_angle_d 0.799 f_chiral_restr 0.05 f_bond_d 0.01 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5461 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 125
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing