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CLIPPER domain from the Gram-negative fibrillar adhesin "B9T28_05395
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 5 mg/mL protein, sample buffer: 20 mM Tris, 100 mM NaCl, pH 8.0, crystallization buffer: 0.2 M Ammonium Sulphate, 0.2 M Sodium/Potassium Tartrate, pH 5.5, droplet size 4 microL at 1:1 protein:crystal buffer ratio, with 1mL crystallization buffer in reservoir.
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.859 α = 90 b = 93.859 β = 90 c = 21.994 γ = 120
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 6M 2023-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9795 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.77 81.285 99.91 0.161 0.993 5.1 38.7 11209 26.87
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.77 1.8 97.16 3.626 0.401 0.4 29.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.77 81.284 11203 569 99.857 0.201 0.2001 0.1979 0.2094 0.2103 32.452
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] -0.616 -0.308 -0.616 1.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.874 r_dihedral_angle_3_deg 14.201 r_scangle_it 7.148 r_lrange_it 6.858 r_scbond_it 5.642 r_dihedral_angle_1_deg 5.416 r_mcangle_it 3.843 r_mcbond_it 3.515 r_angle_refined_deg 1.544 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.874 r_dihedral_angle_3_deg 14.201 r_scangle_it 7.148 r_lrange_it 6.858 r_scbond_it 5.642 r_dihedral_angle_1_deg 5.416 r_mcangle_it 3.843 r_mcbond_it 3.515 r_angle_refined_deg 1.544 r_nbtor_refined 0.301 r_xyhbond_nbd_refined 0.269 r_symmetry_nbd_refined 0.233 r_nbd_refined 0.226 r_symmetry_xyhbond_nbd_refined 0.144 r_chiral_restr 0.066 r_bond_refined_d 0.015 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 871 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2.multiplex data reduction xia2.multiplex data scaling MOLREP phasing