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Crystal structure of Agrobacterium tumefaciens ATU3138 (EFI target 505157), apo structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FFI PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8 experimental model PDB 4DO7 PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8 experimental model PDB 4I6K PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8 experimental model PDB 4DIA PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8 experimental model PDB 4DI8 PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 Protein (10 mg/ml in 20 mM Tris, pH 7.9, 150 mM NaCl, 5 mM MgCl2). Reservoir (0.1 M HEPES, pH 7.5, 20% (w/v) PEG 4000, 10% (w/v) Isopropanol) (MCSG4 G11)). Cryoprotection (Reservoir+20% isopropanol), vapor diffusion, sitting drop, temperature 298K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2 38.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.202 α = 90 b = 77.557 β = 95.49 c = 99.714 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 CCD RAYONIX MX225HE MIRRORS 2013-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 99.257 97.1 0.095 0.095 8.5 3.6 103208 103208 14.25
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 100 0.541 0.541 1.4 3.5 15449
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entries 2ffi,4do7, 4i6k, 4dia, 4di8 1.6 31.598 103114 103114 5138 96.99 0.1486 0.1486 0.1469 0.1487 0.1809 0.1803 RANDOM 20.1631
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 12.611 f_angle_d 1.276 f_chiral_restr 0.075 f_bond_d 0.009 f_plane_restr 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6517 Nucleic Acid Atoms Solvent Atoms 1073 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MOSFLM data reduction PHENIX phasing