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Intramolecular ester bond-containing repeat domain 1 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 0.1 M HEPES, 70% MPD
Crystal Properties Matthews coefficient Solvent content 2.06 40.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.051 α = 90 b = 104.712 β = 91.81 c = 52.587 γ = 90
Symmetry Space Group P 1 21 1
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 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95372 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 1.49 48.09 96.6 0.999 10.5 5.9 81829 18.9
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 1.49 1.52 84.8 0.35 5.4
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 1.49 48.027 78050 4090 97.023 0.169 0.1664 0.1751 0.2121 0.2192 random selection 21.476
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] 0.31 0.098 -0.451 0.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 7.182 r_lrange_it 3.138 r_lrange_other 3.127 r_scangle_it 2.813 r_scangle_other 2.812 r_mcangle_it 2.346 r_mcangle_other 2.346 r_scbond_it 2.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.529 r_dihedral_angle_3_deg 11.578 r_dihedral_angle_1_deg 7.182 r_lrange_it 3.138 r_lrange_other 3.127 r_scangle_it 2.813 r_scangle_other 2.812 r_mcangle_it 2.346 r_mcangle_other 2.346 r_scbond_it 2.324 r_scbond_other 2.297 r_mcbond_it 1.839 r_mcbond_other 1.829 r_angle_other_deg 1.338 r_angle_refined_deg 1.309 r_rigid_bond_restr 1.19 r_symmetry_nbd_refined 0.545 r_nbd_refined 0.183 r_symmetry_nbd_other 0.171 r_nbtor_refined 0.148 r_nbd_other 0.142 r_symmetry_xyhbond_nbd_refined 0.122 r_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.075 r_chiral_restr 0.054 r_bond_refined_d 0.008 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 4164 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing