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Intramolecular ester bond-containing repeat domain 2 from Suipraoptans intestinalis adhesin
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 291 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.075 α = 90 b = 90.603 β = 90 c = 89.686 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2022-08-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.953739 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.46 45.301 99.6 0.999 10.6 13.6 114397
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.49 92.2 0.211 1 12.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 45.301 88757 4410 99.972 0.159 0.1572 0.1682 0.1981 0.2074 random selection 22.769
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] -0.317 0.135 0.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 11.711 r_dihedral_angle_3_deg 10.419 r_dihedral_angle_1_deg 7.113 r_lrange_it 2.928 r_lrange_other 2.834 r_scangle_it 2.485 r_scangle_other 2.484 r_scbond_it 2.003 r_scbond_other 2.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.77 r_dihedral_angle_4_deg 11.711 r_dihedral_angle_3_deg 10.419 r_dihedral_angle_1_deg 7.113 r_lrange_it 2.928 r_lrange_other 2.834 r_scangle_it 2.485 r_scangle_other 2.484 r_scbond_it 2.003 r_scbond_other 2.001 r_mcangle_other 1.883 r_mcangle_it 1.879 r_mcbond_it 1.478 r_mcbond_other 1.447 r_angle_other_deg 1.304 r_angle_refined_deg 1.279 r_rigid_bond_restr 0.984 r_nbd_refined 0.186 r_symmetry_nbd_refined 0.18 r_symmetry_nbd_other 0.171 r_nbd_other 0.157 r_nbtor_refined 0.146 r_xyhbond_nbd_refined 0.111 r_symmetry_xyhbond_nbd_refined 0.089 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.053 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4346 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing