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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 in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 100mM Sodium-citrate, 33% (w/v) PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.08 40.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.182 α = 90 b = 68.182 β = 90 c = 127.412 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 2023-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.96546 ESRF MASSIF-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 1.79 53.64 99.8 0.046 0.051 0.021 0.99 19.3 5.7 17123
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 1.79 1.82 96.8 0.681 0.752 0.314 0.76 5.2
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 1.79 53.63 16292 831 99.72 0.16778 0.16535 0.1774 0.21851 0.2221 RANDOM 27.981
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] -0.58 -0.29 -0.58 1.89
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 18.482 r_long_range_B_other 18.079 r_scangle_other 14.401 r_mcangle_other 12.081 r_mcangle_it 12.074 r_dihedral_angle_3_deg 11.468 r_scbond_it 9.984 r_scbond_other 9.976 r_mcbond_it 8.099 r_mcbond_other 8.086
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 18.482 r_long_range_B_other 18.079 r_scangle_other 14.401 r_mcangle_other 12.081 r_mcangle_it 12.074 r_dihedral_angle_3_deg 11.468 r_scbond_it 9.984 r_scbond_other 9.976 r_mcbond_it 8.099 r_mcbond_other 8.086 r_dihedral_angle_1_deg 5.969 r_rigid_bond_restr 3.912 r_angle_refined_deg 1.427 r_angle_other_deg 0.527 r_dihedral_angle_2_deg 0.258 r_chiral_restr 0.07 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 1012 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing