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Crystal structure of profragilysin-3 (proBFT-3) from Bacteroides fragilis at 1.85 A resolution.
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 18% (w/v) PEG3350, 0.2 M magnesium formate, pH 5.9.
Crystal Properties Matthews coefficient Solvent content 2.5 50.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.72 α = 90 b = 82.74 β = 90 c = 158.9 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 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) 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 1.85 63.07 100 0.999 13.4 13 78068
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 1.85 1.87 0.706
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 1.85 63.07 78068 748 100 0.1888 0.1886 0.185 0.2112 0.207 RANDOM 37.11
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] -0.5808 -1.1451 1.7259
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.9 t_other_torsion 2.63 t_angle_deg 0.91 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 5576 Nucleic Acid Atoms Solvent Atoms 727 Heterogen Atoms 105
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling PHASER phasing