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Crystal structure of a 4-domain construct of LgrA in the substrate donation state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ES5 PDB entry 5ES5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.7 295 Protein + 2.5 mM AMPcPP + 2.5 mM valine + 2 mM N5-fTHF in 2.5 mM magnesium chloride, 15% PEG4000, 100 mM Tris, pH 7.78, 25 mM Tris, pH 7.5, 100 mM sodium chloride equilibrated against a reservoir containing 2.5 mM magnesium chloride, 18% PEG4000, 150 mM sodium chloride, 100 mM Tris, pH 7.7, drops streak-seeded from a seed stock of LgrA (F-A-PCP-C) crystals
Crystal Properties Matthews coefficient Solvent content 2.68 54.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.37 α = 90 b = 133.87 β = 90 c = 162.099 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 100 PIXEL DECTRIS PILATUS3 S 6M 2017-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.979 CLSI 08ID-1
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 2.5 69.333 100 10.1 7.2 50890 40.8
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 2.5 2.58 99.9
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 PDB entry 5ES5 2.5 69.333 1.33 50802 2000 99.94 0.2021 0.2004 0.2003 0.2435 0.2423
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 18.758 f_angle_d 0.672 f_chiral_restr 0.047 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9411 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 109
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing