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Crystal structure of E.coli DsbA in complex with 2-(6-(3-methoxyphenyl)-2-(4-methoxyphenyl)benzofuran-3-yl)acetic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 11-13% PEG 8000, 5-7.5% glycerol, 1 mM copper(II) chloride, 100 mM sodium cacodylate
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.47 α = 90 b = 63.64 β = 125.29 c = 74.34 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM 210r 2016-12-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 2.3 31.82 99.9 0.068 0.079 0.039 0.997 14.3 4 20016
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 2.3 2.38 100 0.325 0.375 0.185 0.91 4.1
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FVK 2.3 31.82 1.34 20007 1107 99.81 0.1931 0.1904 0.1921 0.2382 0.2382 38.227
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 12.551 f_angle_d 1.027 f_chiral_restr 0.052 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2896 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 49
Software Software Software Name Purpose PHENIX refinement Aimless data scaling PDB_EXTRACT data extraction iMOSFLM data reduction PHASER phasing