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Crystal Structure of Escherichia coli GTPase BipA/TypA Complexed with ppGpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 100 mM Tris-HCl, 2 % PEG 6000, and 5 mM [Co(NH3)6]Cl3, pH 8.0
Crystal Properties Matthews coefficient Solvent content 2.85 56.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.821 α = 90 b = 160.125 β = 98.04 c = 89.718 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 ADSC QUANTUM 315r 2014-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.9800 ALS 5.0.1
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 3.31 48.471 98.9 0.17 7 3 23655 70.4
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 3.31 3.58 98.7 0.7 1.8 2.9
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 4ZCI 3.31 48.471 1.36 23602 1128 99.61 0.2354 0.2326 0.24 0.2911 0.2966 104
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 16.211 f_angle_d 1.023 f_chiral_restr 0.036 f_bond_d 0.005 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8477 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 102
Software Software Software Name Purpose MOSFLM data reduction Coot model building MOLREP phasing PHENIX refinement