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X-ray structure of the periplasmic region of PilJ from P. aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YFA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 30% v/v Jeffamine M-600 pH 7.0, 0.1 M Tris pH 8.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.059 α = 90 b = 80.059 β = 90 c = 202.994 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS 2M-F 2018-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 2.32 49.4400799314 99.9 0.068 21.36 7.8 54408 1 64.6291655926
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.32 2.46 1.96 0.45 1.07
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 2yfa 2.50312151016 49.4400799314 1.3400428594 23600 1157 99.9280179532 0.216598906847 0.215074867602 0.2206 0.245240172751 0.2485 67.1813474692
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 19.6691911653 f_angle_d 0.903540805213 f_chiral_restr 0.0531722816143 f_bond_d 0.00856038998807 f_plane_restr 0.00498175339753
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2044 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing