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Burkholderia pseudomallei Disulfide bond forming protein A (DsbA) liganded with fragment 4-methoxy-N-phenylbenzenesulfonamide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4K2D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.1M HEPES pH 7.5
0.2M Li2SO4
29.5% PEG3350
Large excess of 4-methoxy-N-phenylbenzenesulfonamide
Protein concentrated to 33 mgml-1
Crystal Properties Matthews coefficient Solvent content 2.45 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.38 α = 90 b = 59.446 β = 104.862 c = 105.427 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2020-08-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9537 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.31 46.75 97.1 0.1723 0.1871 0.0722 0.994 6.88 6.6 36537 45.07
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.31 2.37 77.9 1.358 1.485 0.5915 0.573 1.05 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 4K2D 2.31 46.75 1.35 35652 1785 97.42 0.2263 0.2276 0.2278 0.2599 0.2612 RANDOM 60.72
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 14.416 f_angle_d 0.5865 f_chiral_restr 0.044 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5844 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing