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Crystal structure of three N-terminal domains of the type V pili tip protein Mfa5 from Porphyromonas gingivalis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6TNJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 17% PEG3350, 80mM NaPO4 pH6, 3mM CaCL and 3mM MgCL
Crystal Properties Matthews coefficient Solvent content 2.76 55.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.72 α = 90 b = 72.81 β = 90 c = 184.49 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 290 PIXEL DECTRIS PILATUS 6M Sagitally bended Si111 crystal 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9756 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.799 46.98 99.45 0.09715 0.1011 0.02756 0.999 19.66 13.1 64113 23.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.799 1.863 95.94 1.126 1.18 0.3445 0.646 1.87 11.1
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 6TNJ 1.8 46.98 1.35 64105 3206 99.46 0.1629 0.161 0.1625 0.1998 0.2007 28.21
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 3.9446 f_angle_d 0.9849 f_chiral_restr 0.0601 f_bond_d 0.0108 f_plane_restr 0.0072
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4351 Nucleic Acid Atoms Solvent Atoms 606 Heterogen Atoms 17
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing BUCCANEER model building