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Bacterial adhesin from Mobiluncus mulieris containing intramolecular disulfide, isopeptide, and ester bond cross-links (space group P1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 10% (v/v) PEG 8000, 20% (v/v) ethylene glycol, 0.02 M carboxylic acids (sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate), and 0.1 M MES/Imidazole (pH 6.5).
Crystal Properties Matthews coefficient Solvent content 2.52 51.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 27.9 α = 67.72 b = 54.983 β = 76.47 c = 57.317 γ = 85.35
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2015-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 1.15 19.15 94.1 1 20.2 7.9 102468
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 1.15 1.17 90.6 0.549 1 7.9
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 (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 in house model 1.15 19.15 97278 5177 94.02 0.18289 0.18141 0.1896 0.21054 0.219 RANDOM 18.59
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] -0.04 -0.02 -0.03 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.625 r_sphericity_free 28.253 r_sphericity_bonded 15.491 r_dihedral_angle_4_deg 12.08 r_dihedral_angle_3_deg 10.51 r_dihedral_angle_1_deg 5.948 r_long_range_B_refined 3.631 r_long_range_B_other 3.396 r_scangle_other 2.575 r_mcangle_it 2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.625 r_sphericity_free 28.253 r_sphericity_bonded 15.491 r_dihedral_angle_4_deg 12.08 r_dihedral_angle_3_deg 10.51 r_dihedral_angle_1_deg 5.948 r_long_range_B_refined 3.631 r_long_range_B_other 3.396 r_scangle_other 2.575 r_mcangle_it 2.47 r_mcangle_other 2.469 r_scbond_it 2.069 r_scbond_other 2.068 r_rigid_bond_restr 1.928 r_mcbond_it 1.858 r_mcbond_other 1.858 r_angle_refined_deg 1.482 r_angle_other_deg 0.842 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2160 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing