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Crystal structure of profragilysin-3 (proBFT-3) from Bacteroides fragilis in complex with hesperetin.
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 22% (w/v) PEG3350,
0.2 M ammonium sulfate
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 2.6 52.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.95 α = 90 b = 83.95 β = 90 c = 266.28 γ = 90
Symmetry Space Group P 41 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 PILATUS 6M-F 2020-02-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91190 Diamond I04-1
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 2.03 80.06 100 0.115 1 23.7 26.4 62673
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 2.03 2.05 2.073 0.83
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 2.03 80.06 62673 747 100 0.2109 0.2108 0.1983 0.2232 0.2181 RANDOM 45.33
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] -1.0961 -1.0961 2.1922
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.69 t_other_torsion 2.64 t_angle_deg 0.9 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_sum_occupancies t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5508 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 122
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing