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Intramolecular ester bond-containing repeat domain from Gemella massiliensis 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, SITTING DROP 291 0.2 M NaCl, 0.1 M Tris.HCl pH 8.0, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.1 41.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.164 α = 90 b = 63.037 β = 90 c = 96.488 γ = 90
Symmetry Space Group P 21 21 21
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 0.95374 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 1.78 48.24 99.5 0.999 9.7 13.2 27465
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 1.78 1.82 91.2 0.449 0.6 11.7
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 1.788 41.643 27103 1307 99.097 0.233 0.2313 0.2355 0.265 0.2673 random selection 34.288
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] -0.922 0.469 0.453
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.781 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 6.936 r_lrange_it 3.24 r_lrange_other 3.234 r_scangle_other 2.245 r_scangle_it 2.238 r_mcangle_it 1.585 r_mcangle_other 1.584 r_scbond_other 1.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.781 r_dihedral_angle_3_deg 11.789 r_dihedral_angle_1_deg 6.936 r_lrange_it 3.24 r_lrange_other 3.234 r_scangle_other 2.245 r_scangle_it 2.238 r_mcangle_it 1.585 r_mcangle_other 1.584 r_scbond_other 1.366 r_scbond_it 1.363 r_mcbond_it 1.005 r_mcbond_other 1.004 r_angle_refined_deg 0.956 r_angle_other_deg 0.326 r_symmetry_nbd_refined 0.273 r_symmetry_xyhbond_nbd_refined 0.234 r_nbd_refined 0.204 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.162 r_nbd_other 0.16 r_xyhbond_nbd_refined 0.122 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.041 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2116 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing