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Crystal Structure of N-terminal flexible domain of the Shaft pilin EbpC from Enterococcus faecalis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9LKS N-terminal domain of Endocarditis and biofilm-associated pilus major subunit EbpC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 100mM CHES-NaOH, pH 9.5 30% (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 1.71 27.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.296 α = 90 b = 67.296 β = 90 c = 108.3 γ = 120
Symmetry Space Group P 61 2 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 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 51.37 94.4 0.072 0.073 0.012 0.99 30.3 34.6 9867
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 2.02 99.2 0.6 0.61 0.1 0.94 5.3 32.5
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 (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 1.99 51.37 9365 502 94.36 0.18636 0.1834 0.1972 0.24192 0.2499 RANDOM 39.633
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] 0.87 0.44 0.87 -2.83
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.3 r_long_range_B_other 23.277 r_scangle_other 15.861 r_mcangle_other 15.007 r_mcangle_it 15.004 r_dihedral_angle_3_deg 12.702 r_scbond_it 10.628 r_scbond_other 10.62 r_mcbond_it 10.209 r_mcbond_other 10.147
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 23.3 r_long_range_B_other 23.277 r_scangle_other 15.861 r_mcangle_other 15.007 r_mcangle_it 15.004 r_dihedral_angle_3_deg 12.702 r_scbond_it 10.628 r_scbond_other 10.62 r_mcbond_it 10.209 r_mcbond_other 10.147 r_dihedral_angle_2_deg 6.328 r_dihedral_angle_1_deg 5.107 r_rigid_bond_restr 3.592 r_angle_refined_deg 1.518 r_angle_other_deg 0.515 r_chiral_restr 0.068 r_bond_refined_d 0.006 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 1030 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing