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Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4DF9 Chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1 M Tris Bicine pH 8.5, 20% Ethylen glycol, 10% PEG 8000, 0.12 M 1,6-Hexanediol, 0.12 M 1-Butanol, 0.12 M 1,2-Propanediol, 0.12 M 2-Propanol, 0.12 M 1,4-Butanediol, 0.12 M 1,3- Propanediol and VPCPVPSTPP peptide 5 mM.
Protein:precipitant ratio 1:1.
Protein concentration: 10 mg/ml.
Protein buffer: 20mM Tris pH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.294 α = 74.16 b = 99.435 β = 88.13 c = 103.386 γ = 82.44
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 PILATUS3 6M 2024-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9786 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.939 29.64 96.95 0.07842 0.04963 0.997 8.67 3.5 271117 33.99
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.94 1.96 88.79 0.9386 0.587 0.425 1.59 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.94 29.64 1.96 271073 13524 96.96 0.1729 0.1709 0.1706 0.2127 0.2123 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.636 f_angle_d 0.989 f_chiral_restr 0.062 f_plane_restr 0.011 f_bond_d 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25694 Nucleic Acid Atoms Solvent Atoms 1375 Heterogen Atoms 225
Software Software Software Name Purpose PHENIX refinement FAST_DP data reduction Aimless data scaling PHASER phasing Coot model building PDB_EXTRACT data extraction