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Crystal structure of a 5-domain construct of LgrA in the substrate donation state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6MFW PDB entry 6MFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 277 0.2 M sodium/potassium phosphate, 22% PEG3350, 0.1 M Bis-Tris propane, pH 7.2
Crystal Properties Matthews coefficient Solvent content 3.04 59.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.863 α = 90 b = 141.114 β = 90 c = 171.532 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 2017-08-10 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) 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 2.5 147.53 99.7 0.095 17.4 12.3 80942 50.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.55 0.475 2
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 6MFW 2.5 85.766 1.39 75813 3793 99.58 0.2395 0.2381 0.2381 0.2664 0.2657
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 16.682 f_angle_d 1.128 f_chiral_restr 0.069 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12694 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 71
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing