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Intramolecular ester bond-containing repeat domain from E. columbae adhesin (split and religated)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NI6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 3.2 M ammonium sulfate, 0.1 M sodium citrate, pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.93 58.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.775 α = 90 b = 120.775 β = 90 c = 45.444 γ = 120
Symmetry Space Group P 6 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 EIGER2 S 16M 2022-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95366 Australian Synchrotron MX2
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 2.37 45.44 99.4 0.187 0.193 0.045 0.998 12 18.6 8323 53.6
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 2.37 2.46 94.5 0.593 0.806 0.9 17.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4NI6 2.373 40.003 8247 401 98.956 0.228 0.226 0.231 0.2614 0.2742 59.756
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] 0.035 0.017 0.035 -0.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.379 r_dihedral_angle_4_deg 23.493 r_dihedral_angle_3_deg 15.439 r_dihedral_angle_1_deg 7.257 r_lrange_it 6.61 r_lrange_other 6.605 r_scangle_it 5.197 r_scangle_other 5.194 r_mcangle_it 3.631 r_mcangle_other 3.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.379 r_dihedral_angle_4_deg 23.493 r_dihedral_angle_3_deg 15.439 r_dihedral_angle_1_deg 7.257 r_lrange_it 6.61 r_lrange_other 6.605 r_scangle_it 5.197 r_scangle_other 5.194 r_mcangle_it 3.631 r_mcangle_other 3.63 r_scbond_it 3.296 r_scbond_other 3.293 r_mcbond_it 2.321 r_mcbond_other 2.317 r_angle_refined_deg 1.299 r_angle_other_deg 1.13 r_nbd_other 0.188 r_nbd_refined 0.182 r_symmetry_nbd_other 0.167 r_symmetry_nbd_refined 0.163 r_nbtor_refined 0.139 r_symmetry_xyhbond_nbd_refined 0.131 r_xyhbond_nbd_refined 0.12 r_symmetry_nbtor_other 0.069 r_chiral_restr 0.037 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1016 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing