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Crystal structure of profragilysin-3 (proBFT-3) from Bacteroides fragilis in complex with foliosidine in P212121.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P24
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277.15 25 % (w/v) PEG 3350
0.2 M ammonium acetate
0.1M Bis Tris pH 5.5
Cryoprotection by soaking for 15-30 seconds in mother liquor supplemented with 2.5M L-proline.
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.55 α = 90 b = 83.06 β = 90 c = 157.48 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 PILATUS 6M 2019-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.7 157.5 98.1 0.184 0.99 9.8 5.7 25344
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.73 0.962 0.73
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 3p24 2.7 73.47 25317 706 98.2 0.2163 0.2155 0.2339 0.2425 0.2619 RANDOM 68.02
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] -4.477 20.0837 -15.6066
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.11 t_other_torsion 3.03 t_angle_deg 0.92 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_utility_distance
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.11 t_other_torsion 3.03 t_angle_deg 0.92 t_bond_d 0.009 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5499 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 78
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing