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Crystal Structure of C-terminal rigid fragment containing middle and C-terminal domains of the Basal pilin EbpB from Enterococcus faecalis.
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 7.5 295 200mM Na/K Phosphate, 100mM Bis-tris pH 7.5, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.91 57.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.538 α = 90 b = 118.538 β = 90 c = 69.781 γ = 120
Symmetry Space Group P 31 2 1
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 2M 2022-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 2.16 102.87 94.4 0.036 0.99 12.4 9.4 17032
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 2.16 2.41 75.4 0.33 0.74 1.9
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.16 102.87 16233 799 55.45 0.1619 0.16052 0.1727 0.19015 0.1864 RANDOM 34.431
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] -1.21 -0.61 -1.21 3.94
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.766 r_long_range_B_other 22.672 r_scangle_other 16.153 r_dihedral_angle_3_deg 15.097 r_dihedral_angle_2_deg 13.737 r_mcangle_other 13.447 r_mcangle_it 13.432 r_scbond_it 10.76 r_scbond_other 10.65 r_mcbond_it 8.681
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 22.766 r_long_range_B_other 22.672 r_scangle_other 16.153 r_dihedral_angle_3_deg 15.097 r_dihedral_angle_2_deg 13.737 r_mcangle_other 13.447 r_mcangle_it 13.432 r_scbond_it 10.76 r_scbond_other 10.65 r_mcbond_it 8.681 r_mcbond_other 8.665 r_dihedral_angle_1_deg 7.373 r_rigid_bond_restr 3.642 r_angle_refined_deg 1.701 r_angle_other_deg 0.547 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1903 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing