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Crystal Structure of C-terminal stable fragment of the Shaft pilin EbpC 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 295 200mM Magnesium Chloride, 100mM Tris- HCl pH 8.5, 25% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.542 α = 91.68 b = 47.6 β = 90.18 c = 125.682 γ = 89.87
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 6M 2024-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.99 125.63 96 0.067 0.08 0.043 0.996 9.2 3.2 50621
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 1.99 2.03 0.466 0.567 0.317 0.817 1.8
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 2 125.63 47860 2671 95.81 0.22468 0.22342 0.2301 0.24839 0.2577 RANDOM 33.852
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] -1.46 0.38 0.14 -1.17 -0.79 2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 11.824 r_dihedral_angle_3_deg 11.343 r_dihedral_angle_1_deg 7.26 r_long_range_B_refined 5.191 r_long_range_B_other 5.191 r_scangle_other 3.113 r_mcangle_it 2.388 r_mcangle_other 2.388 r_scbond_it 2.099 r_scbond_other 2.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 11.824 r_dihedral_angle_3_deg 11.343 r_dihedral_angle_1_deg 7.26 r_long_range_B_refined 5.191 r_long_range_B_other 5.191 r_scangle_other 3.113 r_mcangle_it 2.388 r_mcangle_other 2.388 r_scbond_it 2.099 r_scbond_other 2.098 r_mcbond_it 1.58 r_mcbond_other 1.579 r_angle_refined_deg 1.469 r_angle_other_deg 0.484 r_chiral_restr 0.068 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5903 Nucleic Acid Atoms Solvent Atoms 324 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing